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- PDB-4om0: Crystal structure of antibody VRC07-G54Y in complex with clade A/... -

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Basic information

Entry
Database: PDB / ID: 4om0
TitleCrystal structure of antibody VRC07-G54Y 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-G54Y / 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: 2.289 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 6, 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)89,55613
Polymers87,3443
Non-polymers2,21210
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9290 Å2
ΔGint19 kcal/mol
Surface area35570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.900, 75.528, 198.292
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: 25030.346 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: 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.: 261 / 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: 2.95 Å3/Da / Density % sol: 58.35 %
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-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: 2.2885→50 Å / Num. all: 47196 / Num. obs: 43138 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.098 / Net I/σ(I): 14.5
Reflection shellResolution: 2.2885→2.34 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.543 / % possible all: 53.6

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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: 2.289→37.097 Å / SU ML: 0.33 / σ(F): 1.33 / Phase error: 28.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1998 4.65 %
Rwork0.1914 --
obs0.194 43007 90.45 %
all-47548 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.5 Å2
Refinement stepCycle: LAST / Resolution: 2.289→37.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6039 0 140 261 6440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046345
X-RAY DIFFRACTIONf_angle_d0.8368615
X-RAY DIFFRACTIONf_dihedral_angle_d10.3212299
X-RAY DIFFRACTIONf_chiral_restr0.039978
X-RAY DIFFRACTIONf_plane_restr0.0041105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.289-2.34580.3598750.28741531X-RAY DIFFRACTION48
2.3458-2.40920.3631020.27872086X-RAY DIFFRACTION66
2.4092-2.480.32531220.27452495X-RAY DIFFRACTION78
2.48-2.56010.32391360.2592786X-RAY DIFFRACTION87
2.5601-2.65160.32061460.25752995X-RAY DIFFRACTION93
2.6516-2.75770.32821500.24273094X-RAY DIFFRACTION97
2.7577-2.88310.32251530.23633149X-RAY DIFFRACTION99
2.8831-3.03510.26381550.21983189X-RAY DIFFRACTION99
3.0351-3.22510.24321560.20933208X-RAY DIFFRACTION100
3.2251-3.4740.24151580.20333225X-RAY DIFFRACTION100
3.474-3.82330.22891570.18783250X-RAY DIFFRACTION100
3.8233-4.37580.23671600.16333261X-RAY DIFFRACTION100
4.3758-5.51010.19681610.14153301X-RAY DIFFRACTION100
5.5101-37.10210.21561670.16763439X-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)
13.2477-1.4262-0.37923.4021-1.34433.489-0.1057-0.08480.2131-0.20410.0431-0.52990.20790.350.03530.3805-0.04010.12230.4308-0.09370.425133.042181.04246.3432
22.7629-0.4858-0.82554.00380.06853.819-0.20040.5455-0.2393-0.56910.05590.25320.5789-0.53620.10940.4124-0.13280.01020.4629-0.0920.28210.47779.01564.443
34.2854-0.8454-1.8081.97860.70933.0671-0.01340.18960.16-0.1510.01460.0455-0.1456-0.1853-0.05660.2577-0.0104-0.02560.24670.00390.20565.490294.897426.9604
44.6588-0.3936-0.56172.38520.5823.0177-0.0295-0.2871-0.08340.2894-0.00110.28270.2792-0.14430.0390.3133-0.01930.03040.25220.00310.3735-21.975595.272959.5386
52.4346-0.1432-2.23781.3262-0.57126.77260.026-0.0877-0.09420.0919-0.0696-0.2366-0.01780.11750.03170.1918-0.0102-0.04340.2245-0.00470.302813.031285.345946.4016
66.0531.43452.15683.52210.16294.23520.03370.0688-0.2687-0.2510.13840.39580.282-0.0691-0.17510.352-0.0072-0.00890.163-0.01660.271-15.03380.822960.1469
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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