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- PDB-4olz: Crystal structure of antibody VRC07-G54W in complex with clade A/... -

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Basic information

Entry
Database: PDB / ID: 4olz
TitleCrystal structure of antibody VRC07-G54W 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-G54W / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / 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: 2.1 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.gene_src_common_name ..._chem_comp.pdbx_synonyms / _entity_src_gen.gene_src_common_name / _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
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)89,57913
Polymers87,3673
Non-polymers2,21210
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint17 kcal/mol
Surface area35500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.911, 75.581, 198.398
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: 25053.383 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: 23102.570 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
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


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 14% 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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 60390 / Num. obs: 44387 / % possible obs: 73.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.072 / Net I/σ(I): 22
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.615 / % possible all: 40.8

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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: 2.1→24.993 Å / SU ML: 0.3 / σ(F): 1.33 / Phase error: 32.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 1998 4.52 %
Rwork0.2034 --
obs0.2057 44229 73.19 %
all-60430 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→24.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6041 0 140 241 6422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046387
X-RAY DIFFRACTIONf_angle_d0.8128674
X-RAY DIFFRACTIONf_dihedral_angle_d11.0162312
X-RAY DIFFRACTIONf_chiral_restr0.032982
X-RAY DIFFRACTIONf_plane_restr0.0041113
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15290.3912760.27611623X-RAY DIFFRACTION40
2.1529-2.21110.3056900.26371895X-RAY DIFFRACTION47
2.2111-2.27610.3138980.2612081X-RAY DIFFRACTION51
2.2761-2.34960.34591090.26132286X-RAY DIFFRACTION56
2.3496-2.43350.34331210.2642567X-RAY DIFFRACTION63
2.4335-2.53080.30491310.26042769X-RAY DIFFRACTION68
2.5308-2.64590.32991390.26572914X-RAY DIFFRACTION72
2.6459-2.78520.31431420.25973034X-RAY DIFFRACTION74
2.7852-2.95940.31821480.26793107X-RAY DIFFRACTION76
2.9594-3.18750.2881610.23643398X-RAY DIFFRACTION82
3.1875-3.50750.30571830.22073868X-RAY DIFFRACTION94
3.5075-4.01330.23991950.18644116X-RAY DIFFRACTION99
4.0133-5.04940.20791970.15434205X-RAY DIFFRACTION100
5.0494-24.99470.18472080.17294368X-RAY DIFFRACTION100
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)
12.936-0.9313-0.33293.8964-1.46323.8855-0.1143-0.09230.2213-0.13810.0004-0.72550.2110.44240.09990.2303-0.02420.06790.3936-0.07680.37133.392280.85776.5513
22.4709-0.7717-1.03483.3868-0.01044.2717-0.17230.428-0.2673-0.2850.03250.2770.6031-0.65960.07540.2613-0.13920.01660.4415-0.10210.29810.854979.03264.5193
33.6785-0.9877-0.65882.47930.52292.9756-0.0370.06420.05870.06180.01680.0365-0.31-0.2369-0.00290.2431-0.01770.00110.2545-0.00110.18235.675695.019326.9943
44.7262-0.3710.01512.72370.35313.24840.1246-0.4178-0.07380.3895-0.11210.21070.4328-0.2353-0.0050.3154-0.04580.06040.2207-0.02380.2875-21.926795.336159.3976
53.6088-0.3024-2.95271.2202-0.0868.8238-0.1005-0.103-0.04940.12990.0217-0.19960.10270.24720.08480.2001-0.0002-0.03910.188-0.00150.273313.083284.840745.9087
65.63481.28761.71122.1204-0.00883.6220.00790.164-0.1518-0.15830.16010.38740.3763-0.0208-0.15580.4804-0.0038-0.02460.1515-0.00060.3021-15.052480.891160.0609
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 1:118 )H1 - 118
5X-RAY DIFFRACTION4( CHAIN H AND RESID 119:213 )H119 - 213
6X-RAY DIFFRACTION5( CHAIN L AND RESID 3:108 )L3 - 108
7X-RAY DIFFRACTION6( CHAIN L AND RESID 109:212 )L109 - 212

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