6VN0

BG505 SOSIP.v4.1 in complex with rhesus macaque Fab RM20F

PDB DOI: https://doi.org/10.2210/pdb6VN0/pdb
EM Map EMD-21246: EMDB EMDataResource

Classification: VIRAL PROTEIN/Immune System
Organism(s): Human immunodeficiency virus 1, Macaca mulatta
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2020-01-29 Released: 2020-06-24
Deposition Author(s): Cottrell, C.A., Shin, M., Ward, A.B.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.25 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 308.67 kDa
Atom Count: 19,962
Modelled Residue Count: 2,364
Deposited Residue Count: 2,583
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A, E [auth C], I [auth D]	475	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	B, F [auth E], J [auth F]	153	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
RM20F Fab Heavy Chain	C [auth H], G, K [auth I]	126	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RM20F Kappa Chain	D [auth L], H [auth J], L [auth K]	107	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], IA [auth i], M, MA [auth m], Q, BA [auth b], IA [auth i], M, MA [auth m], Q, X	5		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain IA [auth i] Focus chain M Focus chain MA [auth m] Focus chain Q Focus chain X Interactions & Density Focus chain BA [auth b] Focus chain IA [auth i] Focus chain M Focus chain MA [auth m] Focus chain Q Focus chain X
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], CA [auth c], DA [auth d], EA [auth e], FA [auth f], AA [auth a], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], JA [auth j], KA [auth k], LA [auth l], N, NA [auth n], O, OA [auth o], P, PA [auth p], QA [auth q], R, RA [auth r], S, SA [auth s], T, U, V, W, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain U Focus chain V Focus chain W Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain U Focus chain V Focus chain W Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth E] SDF format, chain FB [auth E] SDF format, chain GB [auth E] SDF format, chain HB [auth D] SDF format, chain IB [auth D] SDF format, chain JB [auth D] SDF format, chain KB [auth D] SDF format, chain LB [auth F] SDF format, chain MB [auth F] SDF format, chain NB [auth F] SDF format, chain TA [auth A] SDF format, chain UA [auth A] SDF format, chain VA [auth A] SDF format, chain WA [auth A] SDF format, chain XA [auth B] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth E] MOL2 format, chain FB [auth E] MOL2 format, chain GB [auth E] MOL2 format, chain HB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain JB [auth D] MOL2 format, chain KB [auth D] MOL2 format, chain LB [auth F] MOL2 format, chain MB [auth F] MOL2 format, chain NB [auth F] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] EB [auth E] AB [auth C], BB [auth C], CB [auth C], DB [auth C], EB [auth E], FB [auth E], GB [auth E], HB [auth D], IB [auth D], JB [auth D], KB [auth D], LB [auth F], MB [auth F], NB [auth F], TA [auth A], UA [auth A], VA [auth A], WA [auth A], XA [auth B], YA [auth B], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth E] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain JB [auth D] Focus chain KB [auth D] Focus chain LB [auth F] Focus chain MB [auth F] Focus chain NB [auth F] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth E] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain JB [auth D] Focus chain KB [auth D] Focus chain LB [auth F] Focus chain MB [auth F] Focus chain NB [auth F] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.25 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Rosetta
MODEL REFINEMENT	Coot
RECONSTRUCTION	cryoSPARC	2

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2020-06-24

Deposition Author(s):

Cottrell, C.A.

Shin, M.

Ward, A.B.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	F31 Al131873
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI144462
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI100663

Revision History (Full details and data files)

Version 1.0: 2020-06-24
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2020-09-16
Changes: Database references, Structure summary

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Help and Resources

6VN0

BG505 SOSIP.v4.1 in complex with rhesus macaque Fab RM20F

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

Entity Groups

Sequence Annotations

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Entity ID: 4

Entity Groups

Sequence Annotations

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Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)