2024-11-13 REL RCSB RCSB RCSB 2016-02-15 2016-03-02 2016-03-02 2024-11-13 Prefusion structure of a human coronavirus spike protein Kirchdoerfer RN Cottrell CA Wang N Pallesen J Yassine HM Turner HL Corbett KS Graham BS McLellan JS Ward AB coronavirus, glycoprotein, prefusion, VIRAL PROTEIN Kirchdoerfer RN Cottrell CA Wang N Pallesen J Yassine HM Turner HL Corbett KS Graham BS McLellan JS Ward AB Pre-fusion structure of a human coronavirus spike protein. Nature UK 531 118 121 2016 26935699 doi:10.1038/nature17200 1476-4687 0006 NATUAS 5i08 FULLOVERLAP HKU1 spike with attached foldon domain and mutated furin-cleavage site HKU1 spike with attached foldon domain and mutated furin-cleavage site 0 1 Human coronavirus HKU1 (isolate N5) 0.42 Spike glycoprotein,Foldon chimera Enterobacteria phage T4 0.144295891 3 Homo sapiens LEVO VIGDFNCTNSFINDYNKTIPRISEDVVDVSLGLGTYYVLNRVYLNTTLLFTGYFPKSGANFRDLALKGSIYLSTLWYKPP FLSDFNNGIFSKVKNTKLYVNNTLYSEFSTIVIGSVFVNTSYTIVVQPHNGILEITACQYTMCEYPHTVCKSKGSIRNES WHIDSSEPLCLFKKNFTYNVSADWLYFHFYQERGVFYAYYADVGMPTTFLFSLYLGTILSHYYVMPLTCNAISSNTDNET LEYWVTPLSRRQYLLNFDEHGVITNAVDCSSSFLSEIQCKTQSFAPNTGVYDLSGFTVKPVATVYRRIPNLPDCDIDNWL NNVSVPSPLNWERRIFSNCNFNLSTLLRLVHVDSFSCNNLDKSKIFGSCFNSITVDKFAIPNRRRDDLQLGSSGFLQSSN YKIDISSSSCQLYYSLPLVNVTINNFNPSSWNRRYGFGSFNLSSYDVVYSDHCFSVNSDFCPCADPSVVNSCAKSKPPSA ICPAGTKYRHCDLDTTLYVKNWCRCSCLPDPISTYSPNTCPQKKVVVGIGEHCPGLGINEEKCGTQLNHSSCFCSPDAFL GWSFDSCISNNRCNIFSNFIFNGINSGTTCSNDLLYSNTEISTGVCVNYDLYGITGQGIFKEVSAAYYNNWQNLLYDSNG NIIGFKDFLTNKTYTILPCYSGRVSAAFYQNSSSPALLYRNLKCSYVLNNISFISQPFYFDSYLGCVLNAVNLTSYSVSS CDLRMGSGFCIDYALPSSGGSGSGISSPYRFVTFEPFNVSFVNDSVETVGGLFEIQIPTNFTIAGHEEFIQTSSPKVTID CSAFVCSNYAACHDLLSEYGTFCDNINSILNEVNDLLDITQLQVANALMQGVTLSSNLNTNLHSDVDNIDFKSLLGCLGS QCGSSSRSLLEDLLFNKVKLSDVGFVEAYNNCTGGSEIRDLLCVQSFNGIKVLPPILSETQISGYTTAATVAAMFPPWSA AAGVPFSLNVQYRINGLGVTMDVLNKNQKLIANAFNKALLSIQNGFTATNSALAKIQSVVNANAQALNSLLQQLFNKFGA ISSSLQEILSRLDNLEAQVQIDRLINGRLTALNAYVSQQLSDITLIKAGASRAIEKVNECVKSQSPRINFCGNGNHILSL VQNAPYGLLFIHFSYKPTSFKTVLVSPGLCLSGDRGIAPKQGYFIKQNDSWMFTGSSYYYPEPISDKNVVFMNSCSVNFT KAPFIYLNNSIPNLSDFEAELSLWFKNHTSIAPNLTFNSHINATFLDLYYEMNVIQESIKSLNGSGYIPEAPRDGQAYVR KDGEWVLLSTFLGLEVLFQ Q0ZME7 P10104 singleParticle particle 0.27 8.0 200.0 NaCl sodium chloride 2.0 C4H11NO3 Tris NEGATIVE uranyl formate
3 uL sample was applied to grid for 30 seconds and then blotted. Grids were stained with 3 uL 1% uranyl formate for 60 seconds followed by blotting.
 EMS CF-2/2-4C C-Flat COPPER 400 CARBON HOLEY PLASMA CLEANING OTHER ETHANE HOMEMADE PLUNGER
3 uL sample was applied to grid, blotted, and plunged into liquid ethane..
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 3.5 22500.0 22500.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 1 1049 10.0 57.0
Images were collected using Legionon and processed using Appion.
 1 39164
2188 particles were selected from a subset of the data using DoG Picker. These particles were used to generate a 3D model from which back projections were derived. Back projection images were used as templates for picking particles from the entire dataset using FindEM.
 Initial model was generated with EMAN2 using a selection of 2D classifications from a subset of the data containing 2188 particles. C3 BACK PROJECTION 4.04 FSC 0.143 CUT-OFF RELION 1.4b1 refine 31435 PROJECTION MATCHING RELION 1.3 PROJECTION MATCHING RELION 1.4b1 629 50.0 IMAGIC MSA emd_8069.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.078518316 0.1497505 0.000042671003 0.005685221 1.31 1.31 1.31 0.0335 AUTHOR None AB INITIO MODEL
Model building and refinement were conducted using a combination of software programs.
EMRinger REAL 117.0 emd_8069_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.02192266 0.07678983 0.000042671003 0.003535451 1.31 1.31 1.31 EMDB None emd_8069_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.021771107 0.04206469 0.000024540042 0.0021651657 1.31 1.31 1.31 EMDB None emd_8069_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.01855608 0.041955918 0.000018130962 0.0021606968 1.31 1.31 1.31 EMDB None