6DFG

BG505 MD39 SOSIP trimer in complex with mature BG18 fragment antigen binding

PDB DOI: https://doi.org/10.2210/pdb6DFG/pdb
EM Map EMD-7875: EMDB EMDataResource

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

Deposited: 2018-05-14 Released: 2019-11-06
Deposition Author(s): Ozorowski, G., Steichen, J.M., Schief, W.R., Ward, A.B.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.42 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 384.56 kDa
Atom Count: 20,190
Modelled Residue Count: 2,355
Deposited Residue Count: 3,255
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]	476	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 gp160	B, F [auth E], J [auth F]	162	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S8 (Human immunodeficiency virus 1) Explore Q2N0S8 Go to UniProtKB: Q2N0S8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S8
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
mature BG18 fragment antigen binding heavy chain	C [auth H], G, K [auth I]	233	Homo sapiens	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
mature BG18 fragment antigen binding light chain	D [auth L], H [auth J], L [auth K]	214	Homo sapiens	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)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	GA [auth g], M, W	4		N-Glycosylation	Interactions Focus chain GA [auth g] Focus chain M Focus chain W Interactions & Density Focus chain GA [auth g] Focus chain M Focus chain W
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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], DA [auth d], FA [auth f], HA [auth h], IA [auth i], AA [auth a], DA [auth d], FA [auth f], HA [auth h], IA [auth i], KA [auth k], N, NA [auth n], O, PA [auth p], Q, T, V, X, Y	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain PA [auth p] Focus chain Q Focus chain T Focus chain V Focus chain X Focus chain Y Interactions & Density Focus chain AA [auth a] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain KA [auth k] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain PA [auth p] Focus chain Q Focus chain T Focus chain V Focus chain X Focus chain Y
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-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	JA [auth j], P, Z	6		N-Glycosylation	Interactions Focus chain JA [auth j] Focus chain P Focus chain Z Interactions & Density Focus chain JA [auth j] Focus chain P Focus chain Z
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], LA [auth l], R	3		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain LA [auth l] Focus chain R Interactions & Density Focus chain BA [auth b] Focus chain LA [auth l] Focus chain R
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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	CA [auth c], MA [auth m], S	10		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain MA [auth m] Focus chain S Interactions & Density Focus chain CA [auth c] Focus chain MA [auth m] Focus chain S
Glycosylation Resources
GlyTouCan: G40702WU GlyCosmos: G40702WU GlyGen: G40702WU

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	EA [auth e], OA [auth o], U	6		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain OA [auth o] Focus chain U Interactions & Density Focus chain EA [auth e] Focus chain OA [auth o] Focus chain U
Glycosylation Resources
GlyTouCan: G01760ZU GlyCosmos: G01760ZU GlyGen: G01760ZU

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 DB [auth D] SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain HB [auth I] SDF format, chain QA [auth A] SDF format, chain RA [auth A] SDF format, chain UA [auth A] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] SDF format, chain BB [auth G] SDF format, chain CB [auth D] SDF format, chain GB [auth D] SDF format, chain SA [auth A] SDF format, chain TA [auth A] SDF format, chain VA [auth H] SDF format, chain WA [auth C] SDF format, chain XA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain DB [auth D] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain HB [auth I] MOL2 format, chain QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain BB [auth G] MOL2 format, chain CB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain SA [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain VA [auth H] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C]	AB [auth C] BB [auth G] CB [auth D] DB [auth D] EB [auth D] AB [auth C], BB [auth G], CB [auth D], DB [auth D], EB [auth D], FB [auth D], GB [auth D], HB [auth I], QA [auth A], RA [auth A], SA [auth A], TA [auth A], UA [auth A], VA [auth H], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth G] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HB [auth I] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth H] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth G] Focus chain CB [auth D] Focus chain DB [auth D] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HB [auth I] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth H] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.42 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.12
MODEL REFINEMENT	Coot	0.8.9
RECONSTRUCTION	RELION	2.1

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2019-11-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI100663
Bill & Melinda Gates Foundation	United States	OPP1115782
Bill & Melinda Gates Foundation	United States	OPP1084519

Revision History (Full details and data files)

Version 1.0: 2019-11-06
Type: Initial release
Version 1.1: 2019-11-13
Changes: Data collection, Database references
Version 1.2: 2019-12-18
Changes: Author supporting evidence, Database references, Other
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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6DFG

BG505 MD39 SOSIP trimer in complex with mature BG18 fragment antigen binding

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

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)