6CRQ

Glutaraldehyde-treated BG505 SOSIP.664 Env in complex with PGV04 Fab

• PDB DOI: https://doi.org/10.2210/pdb6CRQ/pdb
• EM Map EMD-7568: EMDB EMDataResource

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


• Deposited: 2018-03-19 Released: 2018-04-18 
• Deposition Author(s): Pallesen, J., Ward, A.B.
• Funding Organization(s): BMGF, H2020 European AIDS Vaccine Initiative, International AIDS Vaccine Initiative

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 378.14 kDa 
• Atom Count: 20,271 
• Modelled Residue Count: 2,391 
• Deposited Residue Count: 3,207 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A, E [auth B], I [auth F]	480	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus 1) Explore Q2N0S5  Go to UniProtKB:  Q2N0S5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	B [auth C], F [auth G], J [auth H]	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PGV04 VH	C [auth D], G [auth I], K [auth J]	228	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PGV04 VL	D [auth E], H [auth K], L	208	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
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	KA [auth k], M, Y	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

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	BA [auth b], CA [auth c], DA [auth d], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], LA [auth l], N, NA [auth n], OA [auth o], P, PA [auth p], Q, R, RA [auth r], SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, X, Z	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 7
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	AA [auth a], MA [auth m], O	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22573RC GlyCosmos:  G22573RC GlyGen:  G22573RC

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	EA [auth e], QA [auth q], S	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AB [auth C], BB [auth C], CB [auth B], DB [auth B], EB [auth B], FB [auth G], GB [auth G], HB [auth G], IB [auth F], JB [auth F], KB [auth F], LB [auth H], MB [auth H], NB [auth H], WA [auth A], XA [auth A], YA [auth A], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	Rosetta

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-04-18 
Deposition Author(s): Pallesen, J., Ward, A.B.

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Funding Organization	Location	Grant Number
BMGF	United States	OPP1113647
H2020 European AIDS Vaccine Initiative		681137
International AIDS Vaccine Initiative	United States	OPP1084519
International AIDS Vaccine Initiative	United States	OPP1115782

Revision History  

• Version 1.0: 2018-04-18
  Type: Initial release
  
• Version 1.1: 2018-05-23
  Changes: Data collection, Database references
• Version 1.2: 2018-09-19
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2019-12-18
  Changes: Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2022-03-16
  Changes: Author supporting evidence, Database references, Structure summary