2024-10-16 REL PDBe PDBe PDBe 2020-08-19 2021-09-01 2021-09-01 2024-10-16 Wellcome Trust 101908/Z/13/Z United Kingdom Wellcome Trust 217191/Z/19/Z United Kingdom National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01 GM102869-01 United States Envelope glycprotein of endogenous retrovirus Y032 (Atlas virus) from the human hookworm Ancylostoma ceylanicum Mata CP Merchant M class II membrane fusion protein; retroviral envelope protein (Env); lipid binding protein; disulfide bonding, VIRAL PROTEIN Merchant M Mata CP Liu Y Zhai H Protasio AV Modis Y A bioactive phlebovirus-like envelope protein in a hookworm endogenous virus. Sci Adv US 8 eabj6894 eabj6894 2022 35544562 doi:10.1126/sciadv.abj6894 2375-2548 Merchant M Mata CP Liu Y Zhai H Protasio AV Modis Y A bioactive phlebovirus-like envelope protein in a hookworm endogenous virus Biorxiv US 2021 doi:10.1101/2021.11.23.469668 2692-8205 7a4a FULLOVERLAP Viral envelope glycoprotein Viral envelope glycoprotein 0 1
Envelope glycoprotein of endogenous retrovirus Y032 (Atlas virus) from Ancylostoma ceylanicum
Ancylostoma ceylanicum 0.143 Integrase catalytic domain-containing protein Ancylostoma ceylanicum 0.05151909
In chains A, B and C, residue Asn414 is covalently modified with an N-linked N-acetyl glucosamine ligand. Chains A, B and C each contain the following 15 disulfide bonds: Cys1-Cys41, Cys14-Cys23, Cys66-Cys162, Cys87-Cys135, Cys93-Cys142, Cys98-Cys123, Cys127-Cys132, Cys129-Cys138, Cys246-Cys257, Cys264-Cys277, Cys266-Cys275, Cys337-Cys408, Cys347-Cys350, Cys360-Cys382, Cys373-Cys404.
3 Drosophila melanogaster LEVO CSEVISVTSTEEVCTIQENKETCTFNHATTITLQPLQQQTCLTLNDPEKRPMGMLTVKPDGIKFRCNKKIEFFTRDHQIV SESVHRCHRAGSCHSDECHHVKDTDALPEFSSEANSRPGYTSCSSSCGCITCDGCFFCEPSCLFHRLYAIPTTPTIYSIF YCPSWELEVDAEISLQREDETTTSTIRLLPGRTSTWNNIRFSLIGTIVPQLPILSSAFVTNGRQTSIVKPAYAGQLQSNS VGQLQCPNLEAAKQFECHFSRNLCTCTNALHKVSCTCYDGSVEDHMEALPLPQTSKNFLVFEKDRNIYAKTHVGSALQLH IVAQDLKITTVKHTSHCQVEASDLSGCYSCTSGASLTLSCKSDNGEVLANMKCNEQTHVIRCTESGFINNILLMFDTSEV AADCTAACPGGIVNFTIKGLLAFVNERIISQSYSATDVERNIKGKPIPNPLLGLDSTRTGHHHHHH A0A016UZK2 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 3 NAG singleParticle particle 0.025 8.0 20.0 NH12C4O3Cl Tris/HCl 0.1 NaCl sodium chloride 5.0 C3H8O3 glycerol 0.5 C9H15O6P TCEP
20 mM Tris/HCl (NH12C4O3Cl) 0.1 M NaCl 'sodium chloride' 5 % glycerol (C3H8O3) 0.5 mM TCEP (C9H15O6P)
 Quantifoil R1.2/1.3 COPPER 400 CARBON HOLEY GLOW DISCHARGE ETHANE 100 277.2 FEI VITROBOT MARK IV
Grids were blotted for 4 s.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.3 3.5 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN OTHER None None GIF Quantum LS 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1 3027 8.0 46.18
Dose rate = 1.28 e- A^-2 per frame
 1
Movies were motion-corrected and dose-weighted with MOTIONCOR2.
987570
2D references from initial datasets were used to auto-pick the micrographs. One round of reference-free 2D classification was performed to produce templates for better reference-dependent auto-picking.
Micrographs from initial datasets allowed us to obtain a model at 19 A resolution from 3,790 particles. This model was filtered at 40 A resolution and used as the initial model for 3D classification.
 1 C3 FOURIER SPACE 3.76 FSC 0.143 CUT-OFF RELION 3.0 197145 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 4 RELION 3.0 emd_11630.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 234.52802 234.52802 234.52802 90.0 90.0 90.0 X Y Z -0.09405723 0.17276947 -0.000036032765 0.0043969885 1.047 1.047 1.047 0.0153 AUTHOR Final EM map 6EGU A 691-1136 PDB experimental model
A homology model was built from PDB:6EGU using the Swiss-Model server (swissmodel.expasy.org). The model was docked as a rigid body into the density with UCSF Chimera prior to refinement.
 FLEXIBLE FIT
A homology model was built from PDB:6EGU using the Swiss-Model server (swissmodel.expasy.org). The model was docked as a rigid body into the density with UCSF Chimera prior to refinement.
Cross-correlation coefficient REAL 82.0 emd_11630_msk_1.map emd_11630_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 234.52802 234.52802 234.52802 90.0 90.0 90.0 X Y Z -0.019995078 0.04290658 -0.00003635651 0.00196977 1.047 1.047 1.047 AUTHOR Half map 1 emd_11630_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 224 224 224 -112 -112 -112 224 224 224 234.52802 234.52802 234.52802 90.0 90.0 90.0 X Y Z -0.018770304 0.03987026 -0.00003570902 0.001972189 1.047 1.047 1.047 AUTHOR Half map 2