7UR6

Cryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561.DH1021.14 in complex with stabilized HIV-1 Env Ce1176 DS-SOSIP.664

PDB DOI: https://doi.org/10.2210/pdb7UR6/pdb
EM Map EMD-26706: EMDB EMDataResource

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

Deposited: 2022-04-21 Released: 2023-04-26
Deposition Author(s): Gorman, J., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.46 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561.DH1021.14 in complex with stabilized HIV-1 Env Ce1176 DS-SOSIP.664

Gorman, J., Kwong, P.D.

To be published.

Macromolecule Content

Total Structure Weight: 327.1 kDa
Atom Count: 21,633
Modelled Residue Count: 2,466
Deposited Residue Count: 2,610
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gp120	A [auth G], E [auth A], I [auth F]	477	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for C6G0D7 (Human immunodeficiency virus type 1) Explore C6G0D7 Go to UniProtKB: C6G0D7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C6G0D7
Glycosylation
Glycosylation Sites: 24	Glycosylation Focus chain A [auth G] Focus chain E [auth A] Focus chain I [auth F]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
gp41	B, F [auth C], J [auth I]	153	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for C6G0E7 (Human immunodeficiency virus type 1) Explore C6G0E7 Go to UniProtKB: C6G0E7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C6G0E7
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain B Focus chain F [auth C] Focus chain J [auth I]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain	C [auth H], G [auth D], K [auth J]	130	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain	D [auth L], H [auth E], L [auth K]	110	Macaca mulatta	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
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], BA [auth b], BB [auth 1], FA [auth f], GA [auth g], AA [auth a], BA [auth b], BB [auth 1], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], M, N, NA [auth n], OA [auth o], PA [auth p], R, S, T, TA [auth t], U, UA [auth u], V, VA [auth v], W, WA [auth w], XA [auth x], YA [auth y], Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain M Focus chain N Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain R Focus chain S Focus chain T Focus chain TA [auth t] Focus chain U Focus chain UA [auth u] Focus chain V Focus chain VA [auth v] Focus chain W Focus chain WA [auth w] Focus chain XA [auth x] Focus chain YA [auth y] Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain M Focus chain N Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain R Focus chain S Focus chain T Focus chain TA [auth t] Focus chain U Focus chain UA [auth u] Focus chain V Focus chain VA [auth v] Focus chain W Focus chain WA [auth w] Focus chain XA [auth x] Focus chain YA [auth y] Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
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	AB [auth 0], CA [auth c], MA [auth m], O, QA [auth q], AB [auth 0], CA [auth c], MA [auth m], O, QA [auth q], Y	5		N-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain CA [auth c] Focus chain MA [auth m] Focus chain O Focus chain QA [auth q] Focus chain Y Interactions & Density Focus chain AB [auth 0] Focus chain CA [auth c] Focus chain MA [auth m] Focus chain O Focus chain QA [auth q] Focus chain Y
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[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	DA [auth d], P, RA [auth r]	9		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain P Focus chain RA [auth r] Interactions & Density Focus chain DA [auth d] Focus chain P Focus chain RA [auth r]
Glycosylation Resources
GlyTouCan: G83161QT GlyCosmos: G83161QT GlyGen: G83161QT

Entity ID: 8
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	EA [auth e], Q, SA [auth s]	6		N-Glycosylation	Interactions Focus chain EA [auth e] Focus chain Q Focus chain SA [auth s] Interactions & Density Focus chain EA [auth e] Focus chain Q Focus chain SA [auth s]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 9
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	LA [auth l], X, ZA [auth z]	3		N-Glycosylation	Interactions Focus chain LA [auth l] Focus chain X Focus chain ZA [auth z] Interactions & Density Focus chain LA [auth l] Focus chain X Focus chain ZA [auth z]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 AC [auth A] SDF format, chain BC [auth C] SDF format, chain CB [auth G] SDF format, chain CC [auth C] SDF format, chain DB [auth G] SDF format, chain DC [auth C] SDF format, chain EB [auth G] SDF format, chain EC [auth F] SDF format, chain FB [auth G] SDF format, chain FC [auth F] SDF format, chain GB [auth G] SDF format, chain GC [auth F] SDF format, chain HB [auth G] SDF format, chain HC [auth F] SDF format, chain IB [auth G] SDF format, chain IC [auth F] SDF format, chain JB [auth G] SDF format, chain JC [auth F] SDF format, chain KB [auth G] SDF format, chain KC [auth F] SDF format, chain LB [auth G] SDF format, chain LC [auth F] SDF format, chain MB [auth G] SDF format, chain MC [auth F] SDF format, chain NB [auth B] SDF format, chain NC [auth F] SDF format, chain OB [auth B] SDF format, chain OC [auth F] SDF format, chain PB [auth B] SDF format, chain PC [auth I] SDF format, chain QB [auth A] SDF format, chain QC [auth I] SDF format, chain RB [auth A] SDF format, chain RC [auth I] SDF format, chain SB [auth A] SDF format, chain TB [auth A] SDF format, chain UB [auth A] SDF format, chain VB [auth A] SDF format, chain WB [auth A] SDF format, chain XB [auth A] SDF format, chain YB [auth A] SDF format, chain ZB [auth A] MOL2 format, chain AC [auth A] MOL2 format, chain BC [auth C] MOL2 format, chain CB [auth G] MOL2 format, chain CC [auth C] MOL2 format, chain DB [auth G] MOL2 format, chain DC [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain EC [auth F] MOL2 format, chain FB [auth G] MOL2 format, chain FC [auth F] MOL2 format, chain GB [auth G] MOL2 format, chain GC [auth F] MOL2 format, chain HB [auth G] MOL2 format, chain HC [auth F] MOL2 format, chain IB [auth G] MOL2 format, chain IC [auth F] MOL2 format, chain JB [auth G] MOL2 format, chain JC [auth F] MOL2 format, chain KB [auth G] MOL2 format, chain KC [auth F] MOL2 format, chain LB [auth G] MOL2 format, chain LC [auth F] MOL2 format, chain MB [auth G] MOL2 format, chain MC [auth F] MOL2 format, chain NB [auth B] MOL2 format, chain NC [auth F] MOL2 format, chain OB [auth B] MOL2 format, chain OC [auth F] MOL2 format, chain PB [auth B] MOL2 format, chain PC [auth I] MOL2 format, chain QB [auth A] MOL2 format, chain QC [auth I] MOL2 format, chain RB [auth A] MOL2 format, chain RC [auth I] MOL2 format, chain SB [auth A] MOL2 format, chain TB [auth A] MOL2 format, chain UB [auth A] MOL2 format, chain VB [auth A] MOL2 format, chain WB [auth A] MOL2 format, chain XB [auth A] MOL2 format, chain YB [auth A] MOL2 format, chain ZB [auth A] mmCIF format, chain AC [auth A] mmCIF format, chain BC [auth C] mmCIF format, chain CB [auth G] mmCIF format, chain CC [auth C] mmCIF format, chain DB [auth G] mmCIF format, chain DC [auth C] mmCIF format, chain EB [auth G] mmCIF format, chain EC [auth F] mmCIF format, chain FB [auth G] mmCIF format, chain FC [auth F] mmCIF format, chain GB [auth G] mmCIF format, chain GC [auth F] mmCIF format, chain HB [auth G] mmCIF format, chain HC [auth F] mmCIF format, chain IB [auth G] mmCIF format, chain IC [auth F] mmCIF format, chain JB [auth G] mmCIF format, chain JC [auth F] mmCIF format, chain KB [auth G] mmCIF format, chain KC [auth F] mmCIF format, chain LB [auth G] mmCIF format, chain LC [auth F] mmCIF format, chain MB [auth G] mmCIF format, chain MC [auth F] mmCIF format, chain NB [auth B] mmCIF format, chain NC [auth F] mmCIF format, chain OB [auth B] mmCIF format, chain OC [auth F] mmCIF format, chain PB [auth B] mmCIF format, chain PC [auth I] mmCIF format, chain QB [auth A] mmCIF format, chain QC [auth I] mmCIF format, chain RB [auth A] mmCIF format, chain RC [auth I] mmCIF format, chain SB [auth A] mmCIF format, chain TB [auth A] mmCIF format, chain UB [auth A] mmCIF format, chain VB [auth A] mmCIF format, chain WB [auth A] mmCIF format, chain XB [auth A] mmCIF format, chain YB [auth A] mmCIF format, chain ZB [auth A]	AC [auth A] BC [auth C] CB [auth G] CC [auth C] DB [auth G] AC [auth A], BC [auth C], CB [auth G], CC [auth C], DB [auth G], DC [auth C], EB [auth G], EC [auth F], FB [auth G], FC [auth F], GB [auth G], GC [auth F], HB [auth G], HC [auth F], IB [auth G], IC [auth F], JB [auth G], JC [auth F], KB [auth G], KC [auth F], LB [auth G], LC [auth F], MB [auth G], MC [auth F], NB [auth B], NC [auth F], OB [auth B], OC [auth F], PB [auth B], PC [auth I], QB [auth A], QC [auth I], RB [auth A], RC [auth I], SB [auth A], TB [auth A], UB [auth A], VB [auth A], WB [auth A], XB [auth A], YB [auth A], ZB [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AC [auth A] Focus chain BC [auth C] Focus chain CB [auth G] Focus chain CC [auth C] Focus chain DB [auth G] Focus chain DC [auth C] Focus chain EB [auth G] Focus chain EC [auth F] Focus chain FB [auth G] Focus chain FC [auth F] Focus chain GB [auth G] Focus chain GC [auth F] Focus chain HB [auth G] Focus chain HC [auth F] Focus chain IB [auth G] Focus chain IC [auth F] Focus chain JB [auth G] Focus chain JC [auth F] Focus chain KB [auth G] Focus chain KC [auth F] Focus chain LB [auth G] Focus chain LC [auth F] Focus chain MB [auth G] Focus chain MC [auth F] Focus chain NB [auth B] Focus chain NC [auth F] Focus chain OB [auth B] Focus chain OC [auth F] Focus chain PB [auth B] Focus chain PC [auth I] Focus chain QB [auth A] Focus chain QC [auth I] Focus chain RB [auth A] Focus chain RC [auth I] Focus chain SB [auth A] Focus chain TB [auth A] Focus chain UB [auth A] Focus chain VB [auth A] Focus chain WB [auth A] Focus chain XB [auth A] Focus chain YB [auth A] Focus chain ZB [auth A] Interactions & Density Focus chain AC [auth A] Focus chain BC [auth C] Focus chain CB [auth G] Focus chain CC [auth C] Focus chain DB [auth G] Focus chain DC [auth C] Focus chain EB [auth G] Focus chain EC [auth F] Focus chain FB [auth G] Focus chain FC [auth F] Focus chain GB [auth G] Focus chain GC [auth F] Focus chain HB [auth G] Focus chain HC [auth F] Focus chain IB [auth G] Focus chain IC [auth F] Focus chain JB [auth G] Focus chain JC [auth F] Focus chain KB [auth G] Focus chain KC [auth F] Focus chain LB [auth G] Focus chain LC [auth F] Focus chain MB [auth G] Focus chain MC [auth F] Focus chain NB [auth B] Focus chain NC [auth F] Focus chain OB [auth B] Focus chain OC [auth F] Focus chain PB [auth B] Focus chain PC [auth I] Focus chain QB [auth A] Focus chain QC [auth I] Focus chain RB [auth A] Focus chain RC [auth I] Focus chain SB [auth A] Focus chain TB [auth A] Focus chain UB [auth A] Focus chain VB [auth A] Focus chain WB [auth A] Focus chain XB [auth A] Focus chain YB [auth A] Focus chain ZB [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.46 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	2.15
MODEL REFINEMENT	PHENIX	1.20

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-26

Deposition Author(s):

Gorman, J.

Kwong, P.D.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM103310
Other private		Simons Foundation (SF349247)