5V8L

BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibodies 3BNC117 and PGT145

PDB DOI: https://doi.org/10.2210/pdb5V8L/pdb
EM Map EMD-8643: EMDB EMDataResource

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

Deposited: 2017-03-22 Released: 2017-05-03
Deposition Author(s): Lee, J.H., 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: 4.30 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: 440.36 kDa
Atom Count: 22,934
Modelled Residue Count: 2,635
Deposited Residue Count: 3,684
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gp120	A, C, D	481	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
gp41	B, E, 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
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
3BNC117 antibody, heavy chain	G, H, I	226	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT145 antibody, heavy chain	J	267	Homo sapiens	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
3BNC117 antibody, light chain	K, L, M	206	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT145 antibody, light chain	N	219	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: 7
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], AB [auth 0], BA [auth b], BB [auth 1], CA [auth c], AA [auth a], AB [auth 0], BA [auth b], BB [auth 1], CA [auth c], CB [auth 2], DB [auth 3], EA [auth e], EB [auth 4], HA [auth h], IA [auth i], JA [auth j], MA [auth m], NA [auth n], O, OA [auth o], P, PA [auth p], Q, R, RA [auth r], UA [auth u], V, VA [auth v], W, WA [auth w], Z, ZA [auth z]	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain AB [auth 0] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain CA [auth c] Focus chain CB [auth 2] Focus chain DB [auth 3] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain R Focus chain RA [auth r] Focus chain UA [auth u] Focus chain V Focus chain VA [auth v] Focus chain W Focus chain WA [auth w] Focus chain Z Focus chain ZA [auth z] Interactions & Density Focus chain AA [auth a] Focus chain AB [auth 0] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain CA [auth c] Focus chain CB [auth 2] Focus chain DB [auth 3] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain O Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain Q Focus chain R Focus chain RA [auth r] Focus chain UA [auth u] Focus chain V Focus chain VA [auth v] Focus chain W Focus chain WA [auth w] Focus chain Z Focus chain ZA [auth z]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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	DA [auth d], LA [auth l], S, X, YA [auth y]	3		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain LA [auth l] Focus chain S Focus chain X Focus chain YA [auth y] Interactions & Density Focus chain DA [auth d] Focus chain LA [auth l] Focus chain S Focus chain X Focus chain YA [auth y]
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-(1-3)-[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	T	6		N-Glycosylation	Interactions Focus chain T Interactions & Density Focus chain T
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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	U	7		N-Glycosylation	Interactions Focus chain U Interactions & Density Focus chain U
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 11
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	KA [auth k], XA [auth x], Y	5		N-Glycosylation	Interactions Focus chain KA [auth k] Focus chain XA [auth x] Focus chain Y Interactions & Density Focus chain KA [auth k] Focus chain XA [auth x] Focus chain Y
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 12
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	FA [auth f], SA [auth s]	7		N-Glycosylation	Interactions Focus chain FA [auth f] Focus chain SA [auth s] Interactions & Density Focus chain FA [auth f] Focus chain SA [auth s]
Glycosylation Resources
GlyTouCan: G07617FP GlyCosmos: G07617FP GlyGen: G07617FP

Entity ID: 13
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	GA [auth g], QA [auth q], TA [auth t]	8		N-Glycosylation	Interactions Focus chain GA [auth g] Focus chain QA [auth q] Focus chain TA [auth t] Interactions & Density Focus chain GA [auth g] Focus chain QA [auth q] Focus chain TA [auth t]
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

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 FB [auth A] SDF format, chain GB [auth A] SDF format, chain HB [auth A] SDF format, chain JB [auth B] SDF format, chain KB [auth B] SDF format, chain LB [auth B] SDF format, chain MB [auth C] SDF format, chain NB [auth C] SDF format, chain OB [auth C] SDF format, chain PB [auth C] SDF format, chain QB [auth D] SDF format, chain RB [auth D] SDF format, chain SB [auth D] SDF format, chain TB [auth D] SDF format, chain UB [auth D] SDF format, chain VB [auth E] SDF format, chain WB [auth E] SDF format, chain XB [auth F] SDF format, chain YB [auth F] SDF format, chain IB [auth A] MOL2 format, chain FB [auth A] MOL2 format, chain GB [auth A] MOL2 format, chain HB [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain KB [auth B] MOL2 format, chain LB [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain NB [auth C] MOL2 format, chain OB [auth C] MOL2 format, chain PB [auth C] MOL2 format, chain QB [auth D] MOL2 format, chain RB [auth D] MOL2 format, chain SB [auth D] MOL2 format, chain TB [auth D] MOL2 format, chain UB [auth D] MOL2 format, chain VB [auth E] MOL2 format, chain WB [auth E] MOL2 format, chain XB [auth F] MOL2 format, chain YB [auth F] MOL2 format, chain IB [auth A]	FB [auth A] GB [auth A] HB [auth A] IB [auth A] JB [auth B] FB [auth A], GB [auth A], HB [auth A], IB [auth A], JB [auth B], KB [auth B], LB [auth B], MB [auth C], NB [auth C], OB [auth C], PB [auth C], QB [auth D], RB [auth D], SB [auth D], TB [auth D], UB [auth D], VB [auth E], WB [auth E], XB [auth F], YB [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain FB [auth A] Focus chain GB [auth A] Focus chain HB [auth A] Focus chain IB [auth A] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain OB [auth C] Focus chain PB [auth C] Focus chain QB [auth D] Focus chain RB [auth D] Focus chain SB [auth D] Focus chain TB [auth D] Focus chain UB [auth D] Focus chain VB [auth E] Focus chain WB [auth E] Focus chain XB [auth F] Focus chain YB [auth F] Interactions & Density Focus chain FB [auth A] Focus chain GB [auth A] Focus chain HB [auth A] Focus chain IB [auth A] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth C] Focus chain NB [auth C] Focus chain OB [auth C] Focus chain PB [auth C] Focus chain QB [auth D] Focus chain RB [auth D] Focus chain SB [auth D] Focus chain TB [auth D] Focus chain UB [auth D] Focus chain VB [auth E] Focus chain WB [auth E] Focus chain XB [auth F] Focus chain YB [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2017-05-03

Deposition Author(s):

Lee, J.H.

Ward, A.B.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI100663
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01 AI110657
Bill & Melinda Gates Foundation	United States	OPP1115782
Bill & Melinda Gates Foundation	United States	OPP1084519

Revision History (Full details and data files)

Version 1.0: 2017-05-03
Type: Initial release
Version 1.1: 2017-09-13
Changes: Author supporting evidence, Data collection
Version 1.2: 2019-12-11
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, 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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5V8L

BG505 SOSIP.664 trimer in complex with broadly neutralizing HIV antibodies 3BNC117 and PGT145

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

Entity Groups

Sequence Annotations

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Entity ID: 6

Entity Groups

Sequence Annotations

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Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Entity ID: 11

Glycosylation Resources

Entity ID: 12

Glycosylation Resources

Entity ID: 13

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)