6DID

HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1

PDB DOI: https://doi.org/10.2210/pdb6DID/pdb
EM Map EMD-7896: EMDB EMDataResource

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

Deposited: 2018-05-23 Released: 2018-09-05
Deposition Author(s): Turner, H.L., Cottrell, C.A., Oyen, D., Wilson, I.A., 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: 4.71 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: 378.24 kDa
Atom Count: 25,209
Modelled Residue Count: 3,009
Deposited Residue Count: 3,195
Unique protein chains: 4

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A, C [auth F], E [auth G]	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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	B, D [auth I], F [auth J]	153	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S7 (Human immunodeficiency virus 1) Explore Q2N0S7 Go to UniProtKB: Q2N0S7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoclonal antibody 10A light chain	G [auth C], I [auth E], K [auth H]	217	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for P01840 (Oryctolagus cuniculus) Explore P01840 Go to UniProtKB: P01840
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01840
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoclonal antibody 10A heavy chain	H [auth D], J [auth K], L	214	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for A0A1Y1B8B1 (Oryctolagus cuniculus) Explore A0A1Y1B8B1 Go to UniProtKB: A0A1Y1B8B1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Y1B8B1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
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	KA [auth k], M, Y	3		N-Glycosylation	Interactions Focus chain KA [auth k] Focus chain M Focus chain Y Interactions & Density Focus chain KA [auth k] Focus chain M Focus chain Y
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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], BA [auth b], EA [auth e], FA [auth f], GA [auth g], AA [auth a], BA [auth b], EA [auth e], FA [auth f], GA [auth g], JA [auth j], LA [auth l], MA [auth m], N, NA [auth n], O, P, QA [auth q], RA [auth r], S, SA [auth s], T, U, VA [auth v], X, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain JA [auth j] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain P Focus chain QA [auth q] Focus chain RA [auth r] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain U Focus chain VA [auth v] Focus chain X Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain JA [auth j] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain O Focus chain P Focus chain QA [auth q] Focus chain RA [auth r] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain U Focus chain VA [auth v] Focus chain X Focus chain Z
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-(1-3)-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], OA [auth o], Q	7		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain OA [auth o] Focus chain Q Interactions & Density Focus chain CA [auth c] Focus chain OA [auth o] Focus chain Q
Glycosylation Resources
GlyTouCan: G07617FP GlyCosmos: G07617FP GlyGen: G07617FP

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[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	DA [auth d], PA [auth p], R	8		N-Glycosylation	Interactions Focus chain DA [auth d] Focus chain PA [auth p] Focus chain R Interactions & Density Focus chain DA [auth d] Focus chain PA [auth p] Focus chain R
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-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	HA [auth h], TA [auth t], V	6		N-Glycosylation	Interactions Focus chain HA [auth h] Focus chain TA [auth t] Focus chain V Interactions & Density Focus chain HA [auth h] Focus chain TA [auth t] Focus chain V
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	IA [auth i], UA [auth u], W	4		N-Glycosylation	Interactions Focus chain IA [auth i] Focus chain UA [auth u] Focus chain W Interactions & Density Focus chain IA [auth i] Focus chain UA [auth u] Focus chain W
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

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 A] SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain DB [auth F] SDF format, chain EB [auth F] SDF format, chain FB [auth F] SDF format, chain GB [auth F] SDF format, chain HB [auth F] SDF format, chain IB [auth I] SDF format, chain JB [auth I] SDF format, chain KB [auth G] SDF format, chain LB [auth G] SDF format, chain MB [auth G] SDF format, chain NB [auth G] SDF format, chain OB [auth G] SDF format, chain PB [auth J] SDF format, chain QB [auth J] SDF format, chain WA [auth A] SDF format, chain XA [auth A] SDF format, chain YA [auth A] SDF format, chain ZA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain DB [auth F] MOL2 format, chain EB [auth F] MOL2 format, chain FB [auth F] MOL2 format, chain GB [auth F] MOL2 format, chain HB [auth F] MOL2 format, chain IB [auth I] MOL2 format, chain JB [auth I] MOL2 format, chain KB [auth G] MOL2 format, chain LB [auth G] MOL2 format, chain MB [auth G] MOL2 format, chain NB [auth G] MOL2 format, chain OB [auth G] MOL2 format, chain PB [auth J] MOL2 format, chain QB [auth J] MOL2 format, chain WA [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain ZA [auth A]	AB [auth A] BB [auth B] CB [auth B] DB [auth F] EB [auth F] AB [auth A], BB [auth B], CB [auth B], DB [auth F], EB [auth F], FB [auth F], GB [auth F], HB [auth F], IB [auth I], JB [auth I], KB [auth G], LB [auth G], MB [auth G], NB [auth G], OB [auth G], PB [auth J], QB [auth J], WA [auth A], XA [auth A], YA [auth A], ZA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth A] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth F] Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain IB [auth I] Focus chain JB [auth I] Focus chain KB [auth G] Focus chain LB [auth G] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain OB [auth G] Focus chain PB [auth J] Focus chain QB [auth J] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AB [auth A] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain DB [auth F] Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GB [auth F] Focus chain HB [auth F] Focus chain IB [auth I] Focus chain JB [auth I] Focus chain KB [auth G] Focus chain LB [auth G] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain OB [auth G] Focus chain PB [auth J] Focus chain QB [auth J] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.71 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-09-05

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

Revision History (Full details and data files)

Version 1.0: 2018-09-05
Type: Initial release
Version 1.1: 2019-12-18
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

Prepare Data

Validate Data

Deposit Data

Help and Resources

6DID

HIV Env BG505 SOSIP with polyclonal Fabs from immunized rabbit #3417 post-boost#1

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Expand

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)