3U2S | pdb_00003u2s

Crystal Structure of PG9 Fab in Complex with V1V2 Region from HIV-1 strain ZM109

PDB DOI: https://doi.org/10.2210/pdb3U2S/pdb

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

Deposited: 2011-10-04 Released: 2011-11-30
Deposition Author(s): McLellan, J.S., Pancera, M., Kwong, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.205 (Depositor)
R-Value Work:
0.178 (Depositor)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 3.3 of the entry. See complete history.

Literature

Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.

McLellan, J.S., Pancera, M., Carrico, C., Gorman, J., Julien, J.P., Khayat, R., Louder, R., Pejchal, R., Sastry, M., Dai, K., O'Dell, S., Patel, N., Shahzad-Ul-Hussan, S., Yang, Y., Zhang, B., Zhou, T., Zhu, J., Boyington, J.C., Chuang, G.Y., Diwanji, D., Georgiev, I., Do Kwon, Y., Lee, D., Louder, M.K., Moquin, S., Schmidt, S.D., Yang, Z.Y., Bonsignori, M., Crump, J.A., Kapiga, S.H., Sam, N.E., Haynes, B.F., Burton, D.R., Koff, W.C., Walker, L.M., Phogat, S., Wyatt, R., Orwenyo, J., Wang, L.X., Arthos, J., Bewley, C.A., Mascola, J.R., Nabel, G.J., Schief, W.R., Ward, A.B., Wilson, I.A., Kwong, P.D.

(2011) Nature 480: 336-343

PubMed: 22113616 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nature10696
Primary Citation Related Structures:
3TCL, 3U1S, 3U2S, 3U36, 3U46, 3U4B, 3U4E

PubMed Abstract:
Variable regions 1 and 2 (V1/V2) of human immunodeficiency virus-1 (HIV-1) gp120 envelope glycoprotein are critical for viral evasion of antibody neutralization, and are themselves protected by extraordinary sequence diversity and N-linked glycosylation. Human antibodies such as PG9 nonetheless engage V1/V2 and neutralize 80% of HIV-1 isolates. Here we report the structure of V1/V2 in complex with PG9. V1/V2 forms a four-stranded β-sheet domain, in which sequence diversity and glycosylation are largely segregated to strand-connecting loops. PG9 recognition involves electrostatic, sequence-independent and glycan interactions: the latter account for over half the interactive surface but are of sufficiently weak affinity to avoid autoreactivity. The structures of V1/V2-directed antibodies CH04 and PGT145 indicate that they share a common mode of glycan penetration by extended anionic loops. In addition to structurally defining V1/V2, the results thus identify a paradigm of antibody recognition for highly glycosylated antigens, which-with PG9-involves a site of vulnerability comprising just two glycans and a strand.

Organizational Affiliation

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.

Macromolecule Content

Total Structure Weight: 130.61 kDa
Atom Count: 9,160
Modeled Residue Count: 1,059
Deposited Residue Count: 1,176
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PG9 heavy chain	A [auth H], D [auth A]	248	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PG9 light chain	B [auth L], E [auth B]	216	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	C [auth G], F [auth C]	124	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q6TCP8 (Human immunodeficiency virus type 1) Explore Q6TCP8 Go to UniProtKB: Q6TCP8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6TCP8
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C [auth G] Focus chain F [auth C]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[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	G [auth D], H [auth E]	7		N-Glycosylation	Interactions Focus chain G [auth D] Focus chain H [auth E]
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth G] SDF format, chain Q [auth C] MOL2 format, chain L [auth G] MOL2 format, chain Q [auth C] mmCIF format, chain L [auth G] mmCIF format, chain Q [auth C]	L [auth G], Q [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth G] Focus chain Q [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth H] SDF format, chain K [auth L] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain I [auth H] MOL2 format, chain K [auth L] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] mmCIF format, chain I [auth H] mmCIF format, chain K [auth L] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B]	I [auth H], K [auth L], N [auth B], O [auth B], P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth H] Focus chain K [auth L] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
BU3 Query on BU3 Download:Ideal Coordinates CCD File SDF format, chain J [auth L] SDF format, chain M [auth B] MOL2 format, chain J [auth L] MOL2 format, chain M [auth B] mmCIF format, chain J [auth L] mmCIF format, chain M [auth B]	J [auth L], M [auth B]	(R,R)-2,3-BUTANEDIOL C₄ H₁₀ O₂ OWBTYPJTUOEWEK-QWWZWVQMSA-N		Interactions Focus chain J [auth L] Focus chain M [auth B]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A [auth H], D [auth A]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN
TYS Query on TYS	A [auth H], D [auth A]	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.205 (Depositor)
R-Value Work: 0.178 (Depositor)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.465	α = 90
b = 86.565	β = 92.08
c = 94.879	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-11-30

Deposition Author(s):

McLellan, J.S.

Pancera, M.

Kwong, P.D.

Revision History (Full details and data files)

Version 1.0: 2011-11-30
Type: Initial release
Version 1.1: 2011-12-21
Changes: Database references
Version 2.0: 2019-12-25
Changes: Derived calculations, Polymer sequence
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 3.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 3.2: 2023-12-06
Changes: Data collection
Version 3.3: 2024-11-06
Changes: Structure summary