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- PDB-4olv: Crystal structure of antibody VRC07-G54F in complex with clade A/... -

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Basic information

Entry
Database: PDB / ID: 4olv
TitleCrystal structure of antibody VRC07-G54F in complex with clade A/E 93TH057 HIV-1 gp120 core
Components
  • Antigen binding fragment of heavy chain: Antibody VRC01
  • Antigen binding fragment of light chain: Antibody VRC01
  • Envelope glycoprotein gp160
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VRC07 antibody / Passive transfer / Neutralization / In vivo protection / Autoreactivity / Lentiviral infection / Enhanced potency / HIV-1 gp120 / VRC07-G54F / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins ...HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKwon, Y.D. / Kwong, P.D.
CitationJournal: J.Virol. / Year: 2014
Title: Enhanced Potency of a Broadly Neutralizing HIV-1 Antibody In Vitro Improves Protection against Lentiviral Infection In Vivo.
Authors: Rudicell, R.S. / Kwon, Y.D. / Ko, S.Y. / Pegu, A. / Louder, M.K. / Georgiev, I.S. / Wu, X. / Zhu, J. / Boyington, J.C. / Chen, X. / Shi, W. / Yang, Z.Y. / Doria-Rose, N.A. / McKee, K. / ...Authors: Rudicell, R.S. / Kwon, Y.D. / Ko, S.Y. / Pegu, A. / Louder, M.K. / Georgiev, I.S. / Wu, X. / Zhu, J. / Boyington, J.C. / Chen, X. / Shi, W. / Yang, Z.Y. / Doria-Rose, N.A. / McKee, K. / O'Dell, S. / Schmidt, S.D. / Chuang, G.Y. / Druz, A. / Soto, C. / Yang, Y. / Zhang, B. / Zhou, T. / Todd, J.P. / Lloyd, K.E. / Eudailey, J. / Roberts, K.E. / Donald, B.R. / Bailer, R.T. / Ledgerwood, J. / Mullikin, J.C. / Shapiro, L. / Koup, R.A. / Graham, B.S. / Nason, M.C. / Connors, M. / Haynes, B.F. / Rao, S.S. / Roederer, M. / Kwong, P.D. / Mascola, J.R. / Nabel, G.J.
History
DepositionJan 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jun 2, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Envelope glycoprotein gp160
H: Antigen binding fragment of heavy chain: Antibody VRC01
L: Antigen binding fragment of light chain: Antibody VRC01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,74914
Polymers87,3153
Non-polymers2,43311
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint21 kcal/mol
Surface area35850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.180, 75.684, 198.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Envelope glycoprotein gp160


Mass: 39211.434 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 43-122, 201-303, 325-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: 93TH057 / Description: HIV-1 gp120 with leader sequence / Gene: Env, pol / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q0ED31
#2: Antibody Antigen binding fragment of heavy chain: Antibody VRC01


Mass: 25014.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Codon-optimized human antibody heavy chain of VRC01
Gene: Heavy chain / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Antibody Antigen binding fragment of light chain: Antibody VRC01


Mass: 23089.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: Codon-optimized human antibody light chain of VRC01
Gene: Light chain / Plasmid: pVRC8400 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE V1/V2 REGIONS IN CHAIN G WAS REPLACED BY G81, G82. THE V3 REGION IN CHAIN G WAS REPLACED BY THE ...THE V1/V2 REGIONS IN CHAIN G WAS REPLACED BY G81, G82. THE V3 REGION IN CHAIN G WAS REPLACED BY THE REMAINING LINKER GGSGSG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 12% PEG 4000, 0.2M Sodium Acetate, 0.1M Tris 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 36595 / Num. obs: 34696 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.103 / Net I/σ(I): 12.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.577 / % possible all: 57.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3NGB

3ngb


Resolution: 2.5→25.027 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 26.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 1999 5.77 %
Rwork0.2033 --
obs0.2061 34630 94.59 %
all-36610 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→25.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6040 0 154 294 6488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026358
X-RAY DIFFRACTIONf_angle_d0.5828632
X-RAY DIFFRACTIONf_dihedral_angle_d9.482302
X-RAY DIFFRACTIONf_chiral_restr0.027982
X-RAY DIFFRACTIONf_plane_restr0.0031106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.55670.35831200.27811947X-RAY DIFFRACTION80
2.5567-2.62570.28691310.25442144X-RAY DIFFRACTION88
2.6257-2.70290.3151320.26282150X-RAY DIFFRACTION90
2.7029-2.79010.28961360.25192230X-RAY DIFFRACTION92
2.7901-2.88960.31991380.24952241X-RAY DIFFRACTION92
2.8896-3.00510.27961400.24182289X-RAY DIFFRACTION93
3.0051-3.14170.33261420.2262310X-RAY DIFFRACTION95
3.1417-3.3070.30571440.22952371X-RAY DIFFRACTION97
3.307-3.51360.27341480.20662409X-RAY DIFFRACTION99
3.5136-3.78410.24161530.19692474X-RAY DIFFRACTION100
3.7841-4.16330.2411480.1792450X-RAY DIFFRACTION100
4.1633-4.76210.17211530.15922489X-RAY DIFFRACTION100
4.7621-5.98620.22261540.17882511X-RAY DIFFRACTION100
5.9862-25.02790.23441600.19562616X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.28921.64510.79273.0026-1.1383.984-0.10050.0522-0.07440.1615-0.0072-0.3762-0.29630.3380.11080.38330.0404-0.09040.3606-0.06850.337932.3727-5.4635-6.1541
22.53260.49431.02912.9533-0.42273.5761-0.1677-0.46470.23220.2698-0.01280.1671-0.5081-0.57370.11710.45110.1417-0.01350.4655-0.11350.26979.837-3.5611-4.4495
31.9920.34841.42630.58060.24621.67180.0059-0.0279-0.07150.0770.0273-0.0240.1014-0.0818-0.02160.29650.01310.02780.2578-0.0020.24393.7622-19.1292-28.3376
44.4552-0.5166-0.07952.50690.29544.5613-0.00230.31090.0766-0.338-0.020.2938-0.3382-0.1918-0.05790.27710.0171-0.07970.19610.00030.3131-21.6732-19.3693-60.3234
51.8226-0.04462.00710.4792-0.07357.2079-0.02280.04080.0916-0.0993-0.0487-0.1249-0.0651-0.02080.0510.2087-0.00070.030.2128-0.01190.282512.6205-9.7101-47.1406
65.1411-1.2636-1.92992.7030.59933.21980.1119-0.14880.04040.0920.07670.4391-0.3534-0.0749-0.16210.3705-0.00760.0380.18130.02010.2932-16.1861-4.6646-60.2203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN G AND ( RESID 44:252 OR RESID 474:492 ) )G44 - 252
2X-RAY DIFFRACTION1( CHAIN G AND ( RESID 44:252 OR RESID 474:492 ) )G474 - 492
3X-RAY DIFFRACTION2( CHAIN G AND RESID 253:473 )G253 - 473
4X-RAY DIFFRACTION3( CHAIN H AND RESID 1:125 )H1 - 125
5X-RAY DIFFRACTION4( CHAIN H AND RESID 126:216 )H126 - 216
6X-RAY DIFFRACTION5( CHAIN L AND RESID 3:111 )L3 - 111
7X-RAY DIFFRACTION6( CHAIN L AND RESID 112:216 )L112 - 216

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