6CUF

Cryo-EM structure at 4.2 A resolution of vaccine-elicited antibody vFP1.01 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122

PDB DOI: https://doi.org/10.2210/pdb6CUF/pdb
EM Map EMD-7622: EMDB EMDataResource

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

Deposited: 2018-03-26 Released: 2018-07-25
Deposition Author(s): Acharya, P., Carragher, B., Potter, C.S., Kwong, P.D.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.00 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: 539.15 kDa
Atom Count: 32,325
Modelled Residue Count: 3,843
Deposited Residue Count: 4,569
Unique protein chains: 8

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
vFP1.01 heavy chain	A [auth 3], I [auth H], O [auth h]	211	Mus musculus	Mutation(s): 0
Entity Groups
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
vFP1.01 Light chain	B [auth 4], J [auth L], P [auth l]	219	Mus musculus	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
PGT122 Heavy chain	C [auth 5], K [auth M], Q [auth m]	132	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
PGT122 light chain	D [auth 6], L [auth N], R [auth n]	105	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC03 light chain	E [auth 7], N [auth R], T [auth r]	102	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 heavy chain	F [auth 8], M [auth Q], S [auth q]	128	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: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	G [auth C], U [auth 2], X [auth d]	473	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: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	H [auth D], V [auth A], W [auth c]	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

Oligosaccharides

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Entity ID: 9
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	AB [auth t], BB [auth u], LA [auth W], MA [auth X], NA [auth Y], AB [auth t], BB [auth u], LA [auth W], MA [auth X], NA [auth Y], NB [auth DA], Y [auth B], Z [auth E], ZA [auth s]	4		N-Glycosylation	Interactions Focus chain AB [auth t] Focus chain BB [auth u] Focus chain LA [auth W] Focus chain MA [auth X] Focus chain NA [auth Y] Focus chain NB [auth DA] Focus chain Y [auth B] Focus chain Z [auth E] Focus chain ZA [auth s] Interactions & Density Focus chain AB [auth t] Focus chain BB [auth u] Focus chain LA [auth W] Focus chain MA [auth X] Focus chain NA [auth Y] Focus chain NB [auth DA] Focus chain Y [auth B] Focus chain Z [auth E] Focus chain ZA [auth s]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 10
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	AA [auth F], CA [auth I], CB [auth v], EB [auth x], GA [auth P], AA [auth F], CA [auth I], CB [auth v], EB [auth x], GA [auth P], IB [auth 1], OA [auth Z], QA [auth b], UA [auth i]	3		N-Glycosylation	Interactions Focus chain AA [auth F] Focus chain CA [auth I] Focus chain CB [auth v] Focus chain EB [auth x] Focus chain GA [auth P] Focus chain IB [auth 1] Focus chain OA [auth Z] Focus chain QA [auth b] Focus chain UA [auth i] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth I] Focus chain CB [auth v] Focus chain EB [auth x] Focus chain GA [auth P] Focus chain IB [auth 1] Focus chain OA [auth Z] Focus chain QA [auth b] Focus chain UA [auth i]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth G], DB [auth w], EA [auth K], FA [auth O], GB [auth z], BA [auth G], DB [auth w], EA [auth K], FA [auth O], GB [auth z], HB [auth 0], IA [auth T], KA [auth V], KB [auth AA], MB [auth CA], PA [auth a], SA [auth f], TA [auth g], WA [auth k], YA [auth p]	2		N-Glycosylation	Interactions Focus chain BA [auth G] Focus chain DB [auth w] Focus chain EA [auth K] Focus chain FA [auth O] Focus chain GB [auth z] Focus chain HB [auth 0] Focus chain IA [auth T] Focus chain KA [auth V] Focus chain KB [auth AA] Focus chain MB [auth CA] Focus chain PA [auth a] Focus chain SA [auth f] Focus chain TA [auth g] Focus chain WA [auth k] Focus chain YA [auth p] Interactions & Density Focus chain BA [auth G] Focus chain DB [auth w] Focus chain EA [auth K] Focus chain FA [auth O] Focus chain GB [auth z] Focus chain HB [auth 0] Focus chain IA [auth T] Focus chain KA [auth V] Focus chain KB [auth AA] Focus chain MB [auth CA] Focus chain PA [auth a] Focus chain SA [auth f] Focus chain TA [auth g] Focus chain WA [auth k] Focus chain YA [auth p]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 12
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	DA [auth J], FB [auth y], RA [auth e]	6		N-Glycosylation	Interactions Focus chain DA [auth J] Focus chain FB [auth y] Focus chain RA [auth e] Interactions & Density Focus chain DA [auth J] Focus chain FB [auth y] Focus chain RA [auth e]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 13
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	HA [auth S], JB [auth 9], VA [auth j]	5		N-Glycosylation	Interactions Focus chain HA [auth S] Focus chain JB [auth 9] Focus chain VA [auth j] Interactions & Density Focus chain HA [auth S] Focus chain JB [auth 9] Focus chain VA [auth j]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 14
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-(1-3)-[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	JA [auth U], LB [auth BA], XA [auth o]	9		N-Glycosylation	Interactions Focus chain JA [auth U] Focus chain LB [auth BA] Focus chain XA [auth o] Interactions & Density Focus chain JA [auth U] Focus chain LB [auth BA] Focus chain XA [auth o]
Glycosylation Resources
GlyTouCan: G68668TB GlyCosmos: G68668TB GlyGen: G68668TB

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 OB [auth C] SDF format, chain PB [auth C] SDF format, chain QB [auth D] SDF format, chain RB [auth 2] SDF format, chain SB [auth 2] SDF format, chain TB [auth A] SDF format, chain UB [auth c] SDF format, chain VB [auth d] SDF format, chain WB [auth d] MOL2 format, chain OB [auth C] MOL2 format, chain PB [auth C] MOL2 format, chain QB [auth D] MOL2 format, chain RB [auth 2] MOL2 format, chain SB [auth 2] MOL2 format, chain TB [auth A] MOL2 format, chain UB [auth c] MOL2 format, chain VB [auth d] MOL2 format, chain WB [auth d]	OB [auth C] PB [auth C] QB [auth D] RB [auth 2] SB [auth 2] OB [auth C], PB [auth C], QB [auth D], RB [auth 2], SB [auth 2], TB [auth A], UB [auth c], VB [auth d], WB [auth d]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain OB [auth C] Focus chain PB [auth C] Focus chain QB [auth D] Focus chain RB [auth 2] Focus chain SB [auth 2] Focus chain TB [auth A] Focus chain UB [auth c] Focus chain VB [auth d] Focus chain WB [auth d] Interactions & Density Focus chain OB [auth C] Focus chain PB [auth C] Focus chain QB [auth D] Focus chain RB [auth 2] Focus chain SB [auth 2] Focus chain TB [auth A] Focus chain UB [auth c] Focus chain VB [auth d] Focus chain WB [auth d]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.13-2998-000
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-07-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-07-25
Type: Initial release
Version 1.1: 2018-10-03
Changes: Data collection, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, 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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Help and Resources

6CUF

Cryo-EM structure at 4.2 A resolution of vaccine-elicited antibody vFP1.01 in complex with HIV-1 Env BG505 DS-SOSIP, and antibodies VRC03 and PGT122

Entity ID: 1

Entity Groups

Sequence Annotations

Entity ID: 2

Entity Groups

Sequence Annotations

Entity ID: 3

Entity Groups

Sequence Annotations

Entity ID: 4

Entity Groups

Sequence Annotations

Entity ID: 5

Entity Groups

Sequence Annotations

Entity ID: 6

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

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

Entity ID: 14

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)