6E5P

Backbone model based on cryo-EM map at 8.5 A of domain-swapped, glycan-reactive, neutralizing antibody 2G12 bound to HIV-1 Env BG505 DS-SOSIP, which was also bound to CD4-binding site antibody VRC03

PDB DOI: https://doi.org/10.2210/pdb6E5P/pdb
EM Map EMD-8981: EMDB EMDataResource

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

Deposited: 2018-07-21 Released: 2019-02-13
Deposition Author(s): Acharya, P., Kwong, P.D.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 8.80 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: 658.14 kDa
Atom Count: 21,252
Modelled Residue Count: 5,046
Deposited Residue Count: 5,859
Unique protein chains: 6

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2G12 Light chain	A [auth 1] D [auth 4] N [auth K] O [auth L] S [auth Q] A [auth 1], D [auth 4], N [auth K], O [auth L], S [auth Q], V [auth T]	212	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2G12 heavy chain	B [auth 2] C [auth 3] K [auth H] P [auth M] T [auth R] B [auth 2], C [auth 3], K [auth H], P [auth M], T [auth R], U [auth S]	225	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	E [auth A], G [auth C], I [auth E]	474	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	F [auth B], H [auth D], J [auth F]	170	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S9 (Human immunodeficiency virus 1) Explore Q2N0S9 Go to UniProtKB: Q2N0S9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S9
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC03 heavy chain	L [auth I], Q [auth O], W [auth V]	227	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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC03 Light chain	M [auth J], R [auth P], X [auth W]	208	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
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	CA [auth Y], KA [auth g], LA [auth h], MA [auth i], OA [auth k], CA [auth Y], KA [auth g], LA [auth h], MA [auth i], OA [auth k], PA [auth l], SA [auth o], Y [auth G], Z [auth N]	2		N/A	Interactions Focus chain CA [auth Y] Focus chain KA [auth g] Focus chain LA [auth h] Focus chain MA [auth i] Focus chain OA [auth k] Focus chain PA [auth l] Focus chain SA [auth o] Focus chain Y [auth G] Focus chain Z [auth N] Interactions & Density Focus chain CA [auth Y] Focus chain KA [auth g] Focus chain LA [auth h] Focus chain MA [auth i] Focus chain OA [auth k] Focus chain PA [auth l] Focus chain SA [auth o] Focus chain Y [auth G] Focus chain Z [auth N]
Glycosylation Resources
GlyTouCan: G53402KW GlyCosmos: G53402KW GlyGen: G53402KW

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	AA [auth U], NA [auth j], QA [auth m]	6		N/A	Interactions Focus chain AA [auth U] Focus chain NA [auth j] Focus chain QA [auth m] Interactions & Density Focus chain AA [auth U] Focus chain NA [auth j] Focus chain QA [auth m]
Glycosylation Resources
GlyTouCan: G94106MV GlyCosmos: G94106MV GlyGen: G94106MV

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-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	BA [auth X], DA [auth Z], FA [auth b], HA [auth d], JA [auth f], BA [auth X], DA [auth Z], FA [auth b], HA [auth d], JA [auth f], RA [auth n]	7		N/A	Interactions Focus chain BA [auth X] Focus chain DA [auth Z] Focus chain FA [auth b] Focus chain HA [auth d] Focus chain JA [auth f] Focus chain RA [auth n] Interactions & Density Focus chain BA [auth X] Focus chain DA [auth Z] Focus chain FA [auth b] Focus chain HA [auth d] Focus chain JA [auth f] Focus chain RA [auth n]
Glycosylation Resources
GlyTouCan: G92805XC GlyCosmos: G92805XC GlyGen: G92805XC

Entity ID: 10
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	EA [auth a], GA [auth c], IA [auth e]	4		N/A	Interactions Focus chain EA [auth a] Focus chain GA [auth c] Focus chain IA [auth e] Interactions & Density Focus chain EA [auth a] Focus chain GA [auth c] Focus chain IA [auth e]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 7
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900111 Query on PRD_900111	CA [auth G] KA [auth N] LA [auth Y] MA [auth g] OA [auth h] CA [auth G], KA [auth N], LA [auth Y], MA [auth g], OA [auth h], PA [auth i], SA [auth k], Y [auth l], Z [auth o]	2alpha-alpha-mannobiose	Oligosaccharide / Metabolism		Interactions Focus chain CA [auth Y] Focus chain KA [auth g] Focus chain LA [auth h] Focus chain MA [auth i] Focus chain OA [auth k] Focus chain PA [auth l] Focus chain SA [auth o] Focus chain Y [auth G] Focus chain Z [auth N] Interactions & Density Focus chain CA [auth Y] Focus chain KA [auth g] Focus chain LA [auth h] Focus chain MA [auth i] Focus chain OA [auth k] Focus chain PA [auth l] Focus chain SA [auth o] Focus chain Y [auth G] Focus chain Z [auth N]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 8.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-02-13

Deposition Author(s):

Acharya, P.

Kwong, P.D.

Revision History (Full details and data files)

Version 1.0: 2019-02-13
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-03-13
Changes: Data collection, Database references

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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Help and Resources

6E5P

Backbone model based on cryo-EM map at 8.5 A of domain-swapped, glycan-reactive, neutralizing antibody 2G12 bound to HIV-1 Env BG505 DS-SOSIP, which was also bound to CD4-binding site antibody VRC03

Entity ID: 1

Entity Groups

Sequence Annotations

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Entity ID: 2

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 4

UniProt

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: 7

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)