0.018345 0.000000 0.003829 0.000000 0.058962 0.000000 0.000000 0.000000 0.017224 0.00000 0.00000 0.00000 Zhu, Y. Yang, X. Sun, F. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 101.79 90.00 54.510 16.960 59.310 C2 H4 O 44.053 ACETYL GROUP non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking H2 O 18.015 WATER non-polymer C5 H9 N O3 131.130 n 4-HYDROXYPROLINE HYDROXYPROLINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking N 1 N C N 2 N O N 3 N C N 4 N H N 5 N H N 6 N H N 7 N H N 8 N N N 9 S C N 10 N C N 11 N O N 12 N C N 13 N O N 14 N H N 15 N H N 16 N H N 17 N H N 18 N H N 19 N H N 20 N H N 21 N N N 22 N C N 23 N C N 24 N O N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N O N 32 N H N 33 N H N 34 N N N 35 S C N 36 N C N 37 N O N 38 N C N 39 R C N 40 N C N 41 N O N 42 N O N 43 N H N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N H N 50 N H N 51 N H N 52 N N N 53 S C N 54 N C N 55 N O N 56 N C N 57 N C N 58 N C N 59 N C N 60 N N N 61 N O N 62 N H N 63 N H N 64 N H N 65 N H N 66 N H N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N H N 75 N H N 76 N H N 77 N N N 78 S C N 79 N C N 80 N O N 81 N C N 82 N C N 83 N S N 84 N C N 85 N O N 86 N H N 87 N H N 88 N H N 89 N H N 90 N H N 91 N H N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N N N 98 S C N 99 N C N 100 N O N 101 N C N 102 N C N 103 N C N 104 N O N 105 N H N 106 N H N 107 N H N 108 N H N 109 N H N 110 N H N 111 N H N 112 N H N 113 N H N 1 N doub N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N sing N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N doub N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N doub N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N doub N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N doub N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N doub N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N doub N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing To Be Published 0353 Structure of a triple-helix region of human collagen type VIII 10.2210/pdb9vme/pdb pdb_00009vme 100 1 N PIXEL 2025-06-26 RIGAKU HyPix-3000 SINGLE WAVELENGTH M x-ray 1 1.54187 1.0 1.54187 ROTATING ANODE RIGAKU MICROMAX-007 HF 2449.738 A triple-helix region of human collagen type VIII 3 man polymer 18.015 water 114 nat water no yes (ACE)P(HYP)GP(HYP)GP(HYP)GAMGMPGAKGP(HYP)GP(HYP)GP(HYP)G XPPGPPGPPGAMGMPGAKGPPGPPGPPG A,B,C polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n sample 1 28 9606 Homo sapiens 32630 synthetic construct Biological sequence 1 1.83 32.63 VAPOR DIFFUSION, HANGING DROP 0.05 M Ammonium Sulfate, 0.05 M Bis-Tris: HCl, pH 6.5, 30 % (v/v) Pentaerythritol Ethoxylate (15/4_EO/OH) 289 repository Initial release 1 0 2026-07-01 Not funded feisun@ibp.ac.cn 0000-0002-0351-5144 Fei Sun principal investigator/group leader N PDBJ Y PDBC 2025-06-27 REL REL HOH water N Y AlphaFold in silico model A HYP 2 Named protein modification A HYP 3 PRO HYP 1 1_555 Hydroxylation A HYP 5 Named protein modification A HYP 6 PRO HYP 1 1_555 Hydroxylation A HYP 8 Named protein modification A HYP 9 PRO HYP 1 1_555 Hydroxylation A HYP 20 Named protein modification A HYP 21 PRO HYP 1 1_555 Hydroxylation A HYP 23 Named protein modification A HYP 24 PRO HYP 1 1_555 Hydroxylation A HYP 26 Named protein modification A HYP 27 PRO HYP 1 1_555 Hydroxylation B HYP 2 Named protein modification B HYP 3 PRO HYP 1 1_555 Hydroxylation B HYP 5 Named protein modification B HYP 6 PRO HYP 1 1_555 Hydroxylation B HYP 8 Named protein modification B HYP 9 PRO HYP 1 1_555 Hydroxylation B HYP 20 Named protein modification B HYP 21 PRO HYP 1 1_555 Hydroxylation B HYP 23 Named protein modification B HYP 24 PRO HYP 1 1_555 Hydroxylation B HYP 26 Named protein modification B HYP 27 PRO HYP 1 1_555 Hydroxylation C HYP 2 Named protein modification C HYP 3 PRO HYP 1 1_555 Hydroxylation C HYP 5 Named protein modification C HYP 6 PRO HYP 1 1_555 Hydroxylation C HYP 8 Named protein modification C HYP 9 PRO HYP 1 1_555 Hydroxylation C HYP 20 Named protein modification C HYP 21 PRO HYP 1 1_555 Hydroxylation C HYP 23 Named protein modification C HYP 24 PRO HYP 1 1_555 Hydroxylation C HYP 26 Named protein modification C HYP 27 PRO HYP 1 1_555 Hydroxylation A ACE 0 Terminal acetylation A ACE 1 A PRO 1 PRO A PRO 2 1_555 ACE 13 1_555 None B ACE 0 Terminal acetylation B ACE 1 B PRO 1 PRO B PRO 2 1_555 ACE 13 1_555 None C ACE 0 Terminal acetylation C ACE 1 C PRO 1 PRO C PRO 2 1_555 ACE 13 1_555 None HOH 144 2 HOH HOH 101 A HOH 98 2 HOH HOH 102 A HOH 64 2 HOH HOH 103 A HOH 75 2 HOH HOH 104 A HOH 133 2 HOH HOH 105 A HOH 114 2 HOH HOH 106 A HOH 135 2 HOH HOH 107 A HOH 78 2 HOH HOH 108 A HOH 72 2 HOH HOH 109 A HOH 3 2 HOH HOH 110 A HOH 1 2 HOH HOH 111 A HOH 97 2 HOH HOH 112 A HOH 93 2 HOH HOH 113 A HOH 49 2 HOH HOH 114 A HOH 31 2 HOH HOH 115 A HOH 47 2 HOH HOH 116 A HOH 23 2 HOH HOH 117 A HOH 154 2 HOH HOH 118 A HOH 125 2 HOH HOH 119 A HOH 2 2 HOH HOH 120 A HOH 43 2 HOH HOH 121 A HOH 11 2 HOH HOH 122 A HOH 100 2 HOH HOH 123 A HOH 110 2 HOH HOH 124 A HOH 39 2 HOH HOH 125 A HOH 61 2 HOH HOH 126 A HOH 58 2 HOH HOH 127 A HOH 17 2 HOH HOH 128 A HOH 27 2 HOH HOH 129 A HOH 36 2 HOH HOH 130 A HOH 24 2 HOH HOH 131 A HOH 51 2 HOH HOH 132 A HOH 102 2 HOH HOH 133 A HOH 123 2 HOH HOH 134 A HOH 130 2 HOH HOH 135 A HOH 156 2 HOH HOH 136 A HOH 32 2 HOH HOH 137 A HOH 160 2 HOH HOH 138 A HOH 132 2 HOH HOH 139 A HOH 119 2 HOH HOH 140 A HOH 155 2 HOH HOH 141 A HOH 127 2 HOH HOH 142 A HOH 162 2 HOH HOH 143 A HOH 90 2 HOH HOH 144 A HOH 149 2 HOH HOH 145 A HOH 66 2 HOH HOH 146 A HOH 116 2 HOH HOH 147 A HOH 138 2 HOH HOH 148 A HOH 7 2 HOH HOH 101 B HOH 80 2 HOH HOH 102 B HOH 141 2 HOH HOH 103 B HOH 4 2 HOH HOH 104 B HOH 101 2 HOH HOH 105 B HOH 153 2 HOH HOH 106 B HOH 124 2 HOH HOH 107 B HOH 139 2 HOH HOH 108 B HOH 111 2 HOH HOH 109 B HOH 20 2 HOH HOH 110 B HOH 52 2 HOH HOH 111 B HOH 74 2 HOH HOH 112 B HOH 86 2 HOH HOH 113 B HOH 126 2 HOH HOH 114 B HOH 146 2 HOH HOH 115 B HOH 118 2 HOH HOH 116 B HOH 150 2 HOH HOH 117 B HOH 18 2 HOH HOH 118 B HOH 79 2 HOH HOH 119 B HOH 166 2 HOH HOH 120 B HOH 122 2 HOH HOH 121 B HOH 62 2 HOH HOH 122 B HOH 112 2 HOH HOH 123 B HOH 99 2 HOH HOH 124 B HOH 113 2 HOH HOH 125 B HOH 89 2 HOH HOH 126 B HOH 69 2 HOH HOH 127 B HOH 81 2 HOH HOH 128 B HOH 68 2 HOH HOH 129 B HOH 91 2 HOH HOH 130 B HOH 143 2 HOH HOH 131 B HOH 44 2 HOH HOH 101 C HOH 21 2 HOH HOH 102 C HOH 115 2 HOH HOH 103 C HOH 8 2 HOH HOH 104 C HOH 10 2 HOH HOH 105 C HOH 67 2 HOH HOH 106 C HOH 19 2 HOH HOH 107 C HOH 175 2 HOH HOH 108 C HOH 42 2 HOH HOH 109 C HOH 106 2 HOH HOH 110 C HOH 34 2 HOH HOH 111 C HOH 159 2 HOH HOH 112 C HOH 157 2 HOH HOH 113 C HOH 82 2 HOH HOH 114 C HOH 12 2 HOH HOH 115 C HOH 33 2 HOH HOH 116 C HOH 50 2 HOH HOH 117 C HOH 48 2 HOH HOH 118 C HOH 40 2 HOH HOH 119 C HOH 14 2 HOH HOH 120 C HOH 170 2 HOH HOH 121 C HOH 53 2 HOH HOH 122 C HOH 145 2 HOH HOH 123 C HOH 9 2 HOH HOH 124 C HOH 168 2 HOH HOH 125 C HOH 104 2 HOH HOH 126 C HOH 45 2 HOH HOH 127 C HOH 167 2 HOH HOH 128 C HOH 65 2 HOH HOH 129 C HOH 55 2 HOH HOH 130 C HOH 137 2 HOH HOH 131 C HOH 6 2 HOH HOH 132 C HOH 134 2 HOH HOH 133 C HOH 129 2 HOH HOH 134 C HOH 164 2 HOH HOH 135 C ACE 0 n 1 ACE 0 A PRO 1 n 2 PRO 1 A HYP 2 n 3 HYP 2 A GLY 3 n 4 GLY 3 A PRO 4 n 5 PRO 4 A HYP 5 n 6 HYP 5 A GLY 6 n 7 GLY 6 A PRO 7 n 8 PRO 7 A HYP 8 n 9 HYP 8 A GLY 9 n 10 GLY 9 A ALA 10 n 11 ALA 10 A MET 11 n 12 MET 11 A GLY 12 n 13 GLY 12 A MET 13 n 14 MET 13 A PRO 14 n 15 PRO 14 A GLY 15 n 16 GLY 15 A ALA 16 n 17 ALA 16 A LYS 17 n 18 LYS 17 A GLY 18 n 19 GLY 18 A PRO 19 n 20 PRO 19 A HYP 20 n 21 HYP 20 A GLY 21 n 22 GLY 21 A PRO 22 n 23 PRO 22 A HYP 23 n 24 HYP 23 A GLY 24 n 25 GLY 24 A PRO 25 n 26 PRO 25 A HYP 26 n 27 HYP 26 A GLY 27 n 28 GLY 27 A ACE 0 n 1 ACE 0 B PRO 1 n 2 PRO 1 B HYP 2 n 3 HYP 2 B GLY 3 n 4 GLY 3 B PRO 4 n 5 PRO 4 B HYP 5 n 6 HYP 5 B GLY 6 n 7 GLY 6 B PRO 7 n 8 PRO 7 B HYP 8 n 9 HYP 8 B GLY 9 n 10 GLY 9 B ALA 10 n 11 ALA 10 B MET 11 n 12 MET 11 B GLY 12 n 13 GLY 12 B MET 13 n 14 MET 13 B PRO 14 n 15 PRO 14 B GLY 15 n 16 GLY 15 B ALA 16 n 17 ALA 16 B LYS 17 n 18 LYS 17 B GLY 18 n 19 GLY 18 B PRO 19 n 20 PRO 19 B HYP 20 n 21 HYP 20 B GLY 21 n 22 GLY 21 B PRO 22 n 23 PRO 22 B HYP 23 n 24 HYP 23 B GLY 24 n 25 GLY 24 B PRO 25 n 26 PRO 25 B HYP 26 n 27 HYP 26 B GLY 27 n 28 GLY 27 B ACE 0 n 1 ACE 0 C PRO 1 n 2 PRO 1 C HYP 2 n 3 HYP 2 C GLY 3 n 4 GLY 3 C PRO 4 n 5 PRO 4 C HYP 5 n 6 HYP 5 C GLY 6 n 7 GLY 6 C PRO 7 n 8 PRO 7 C HYP 8 n 9 HYP 8 C GLY 9 n 10 GLY 9 C ALA 10 n 11 ALA 10 C MET 11 n 12 MET 11 C GLY 12 n 13 GLY 12 C MET 13 n 14 MET 13 C PRO 14 n 15 PRO 14 C GLY 15 n 16 GLY 15 C ALA 16 n 17 ALA 16 C LYS 17 n 18 LYS 17 C GLY 18 n 19 GLY 18 C PRO 19 n 20 PRO 19 C HYP 20 n 21 HYP 20 C GLY 21 n 22 GLY 21 C PRO 22 n 23 PRO 22 C HYP 23 n 24 HYP 23 C GLY 24 n 25 GLY 24 C PRO 25 n 26 PRO 25 C HYP 26 n 27 HYP 26 C GLY 27 n 28 GLY 27 C 1.4935 -0.6074 -3.7442 -0.0222 1.4612 6.8645 -0.4985 0.0262 -0.1223 0.2149 0.0302 0.0471 0.8620 0.0838 -0.0573 0.1122 0.0237 -0.0565 0.1244 -0.0148 0.0921 refined 20.1442 10.4159 -19.7861 X-RAY DIFFRACTION 1.2964 0.0546 -1.7883 -0.0358 0.5250 2.0968 0.1073 -0.2225 -0.0868 -0.0554 -0.0323 0.0001 -0.3410 0.3256 0.0049 0.0962 0.0099 -0.0222 0.0668 0.0024 0.0988 refined 21.1191 10.2718 -22.5579 X-RAY DIFFRACTION 1.0322 -0.0565 -3.5628 -0.3060 -0.5897 7.5526 -0.3919 0.3227 -0.5373 0.0809 -0.2781 -0.0489 0.4360 -0.7467 0.0735 0.1613 -0.0765 0.0215 0.0730 -0.0122 0.1330 refined 18.8736 10.1109 -17.2729 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 (chain 'B' and resid 0 through 27) X-RAY DIFFRACTION 2 (chain 'C' and resid 0 through 27) X-RAY DIFFRACTION 3 (chain 'A' and resid 0 through 27) author_and_software_defined_assembly PISA 3 trimeric assay for oligomerization 5240 -31 4820 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A A O O HOH HOH 113 123 1.80 1 C C O O HOH HOH 130 132 1.82 1 A A O O HOH HOH 116 135 2.03 1 C C NZ O LYS HOH 17 101 2.09 1 A A O O HOH HOH 125 142 2.19 1 B C O O HOH HOH 128 126 2.15 1_555 1_565 1 A A O O HOH HOH 136 147 2.19 1_555 4_554 0.2229 0.1892 0.1911 1.94 22.56 185 3890 4.76 93.40 0.09 1 FREE R-VALUE 1.45 MOLECULAR REPLACEMENT 17.46 0.90 1.10 ML FLAT BULK SOLVENT MODEL 1.94 22.56 114 627 0 0 513 0.003 549 0.846 756 15.081 195 0.070 72 0.003 99 0.2229 0.1892 22.56 185 3705 93.00 1.94 22.56 9VME 3896 0.999 1 36.34 7.2 93.40 1.94 2.00 258 0.995 1 refinement PHENIX 1.21.1 data scaling Aimless data reduction iMOSFLM phasing PHASER data extraction PDB_EXTRACT N Structure of a triple-helix region of human collagen type VIII 1 N N 1 N N 1 N N 2 N N 2 N N 2 N N covale 1.332 both A ACE 0 A C ACE 1 1_555 A PRO 1 A N PRO 2 1_555 covale 1.329 both A PRO 1 A C PRO 2 1_555 A HYP 2 A N HYP 3 1_555 covale 1.327 both A HYP 2 A C HYP 3 1_555 A GLY 3 A N GLY 4 1_555 covale 1.331 both A PRO 4 A C PRO 5 1_555 A HYP 5 A N HYP 6 1_555 covale 1.327 both A HYP 5 A C HYP 6 1_555 A GLY 6 A N GLY 7 1_555 covale 1.328 both A PRO 7 A C PRO 8 1_555 A HYP 8 A N HYP 9 1_555 covale 1.329 both A HYP 8 A C HYP 9 1_555 A GLY 9 A N GLY 10 1_555 covale 1.329 both A PRO 19 A C PRO 20 1_555 A HYP 20 A N HYP 21 1_555 covale 1.329 both A HYP 20 A C HYP 21 1_555 A GLY 21 A N GLY 22 1_555 covale 1.330 both A PRO 22 A C PRO 23 1_555 A HYP 23 A N HYP 24 1_555 covale 1.328 both A HYP 23 A C HYP 24 1_555 A GLY 24 A N GLY 25 1_555 covale 1.330 both A PRO 25 A C PRO 26 1_555 A HYP 26 A N HYP 27 1_555 covale 1.329 both A HYP 26 A C HYP 27 1_555 A GLY 27 A N GLY 28 1_555 covale 1.331 both B ACE 0 B C ACE 1 1_555 B PRO 1 B N PRO 2 1_555 covale 1.329 both B PRO 1 B C PRO 2 1_555 B HYP 2 B N HYP 3 1_555 covale 1.327 both B HYP 2 B C HYP 3 1_555 B GLY 3 B N GLY 4 1_555 covale 1.330 both B PRO 4 B C PRO 5 1_555 B HYP 5 B N HYP 6 1_555 covale 1.328 both B HYP 5 B C HYP 6 1_555 B GLY 6 B N GLY 7 1_555 covale 1.331 both B PRO 7 B C PRO 8 1_555 B HYP 8 B N HYP 9 1_555 covale 1.325 both B HYP 8 B C HYP 9 1_555 B GLY 9 B N GLY 10 1_555 covale 1.330 both B PRO 19 B C PRO 20 1_555 B HYP 20 B N HYP 21 1_555 covale 1.328 both B HYP 20 B C HYP 21 1_555 B GLY 21 B N GLY 22 1_555 covale 1.328 both B PRO 22 B C PRO 23 1_555 B HYP 23 B N HYP 24 1_555 covale 1.327 both B HYP 23 B C HYP 24 1_555 B GLY 24 B N GLY 25 1_555 covale 1.328 both B PRO 25 B C PRO 26 1_555 B HYP 26 B N HYP 27 1_555 covale 1.328 both B HYP 26 B C HYP 27 1_555 B GLY 27 B N GLY 28 1_555 covale 1.334 both C ACE 0 C C ACE 1 1_555 C PRO 1 C N PRO 2 1_555 covale 1.328 both C PRO 1 C C PRO 2 1_555 C HYP 2 C N HYP 3 1_555 covale 1.327 both C HYP 2 C C HYP 3 1_555 C GLY 3 C N GLY 4 1_555 covale 1.330 both C PRO 4 C C PRO 5 1_555 C HYP 5 C N HYP 6 1_555 covale 1.328 both C HYP 5 C C HYP 6 1_555 C GLY 6 C N GLY 7 1_555 covale 1.328 both C PRO 7 C C PRO 8 1_555 C HYP 8 C N HYP 9 1_555 covale 1.328 both C HYP 8 C C HYP 9 1_555 C GLY 9 C N GLY 10 1_555 covale 1.330 both C PRO 19 C C PRO 20 1_555 C HYP 20 C N HYP 21 1_555 covale 1.328 both C HYP 20 C C HYP 21 1_555 C GLY 21 C N GLY 22 1_555 covale 1.330 both C PRO 22 C C PRO 23 1_555 C HYP 23 C N HYP 24 1_555 covale 1.327 both C HYP 23 C C HYP 24 1_555 C GLY 24 C N GLY 25 1_555 covale 1.329 both C PRO 25 C C PRO 26 1_555 C HYP 26 C N HYP 27 1_555 covale 1.328 both C HYP 26 C C HYP 27 1_555 C GLY 27 C N GLY 28 1_555 STRUCTURAL PROTEIN Collagen, STRUCTURAL PROTEIN 9VME PDB 1 1 9VME 0 27 9VME 0 27 9VME A 1 1 28 0 27 9VME 0 27 9VME B 1 1 28 0 27 9VME 0 27 9VME C 1 1 28 5 C 1 2 1