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- PDB-4jb9: Crystal structure of antibody VRC06 in complex with HIV-1 gp120 core -

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Basic information

Entry
Database: PDB / ID: 4jb9
TitleCrystal structure of antibody VRC06 in complex with HIV-1 gp120 core
Components
  • antibody VRC06 heavy chain
  • antibody VRC06 light chain
  • clade A/E 93TH057 HIV-1 gp120 core
Keywordsviral protein/immune system / HIV-1 / gp120 / antibody / VRC06 / glycoprotein / IMMUNE SYSTEM / viral protein-immune system complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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 / SAD / Resolution: 2.6 Å
AuthorsKwon, Y.D. / Zhou, T. / Srivatsan, S. / Kwong, P.D.
CitationJournal: Science / Year: 2013
Title: Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization.
Authors: Georgiev, I.S. / Doria-Rose, N.A. / Zhou, T. / Kwon, Y.D. / Staupe, R.P. / Moquin, S. / Chuang, G.Y. / Louder, M.K. / Schmidt, S.D. / Altae-Tran, H.R. / Bailer, R.T. / McKee, K. / Nason, M. ...Authors: Georgiev, I.S. / Doria-Rose, N.A. / Zhou, T. / Kwon, Y.D. / Staupe, R.P. / Moquin, S. / Chuang, G.Y. / Louder, M.K. / Schmidt, S.D. / Altae-Tran, H.R. / Bailer, R.T. / McKee, K. / Nason, M. / O'Dell, S. / Ofek, G. / Pancera, M. / Srivatsan, S. / Shapiro, L. / Connors, M. / Migueles, S.A. / Morris, L. / Nishimura, Y. / Martin, M.A. / Mascola, J.R. / Kwong, P.D.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Oct 19, 2016Group: Other
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: clade A/E 93TH057 HIV-1 gp120 core
H: antibody VRC06 heavy chain
L: antibody VRC06 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,80113
Polymers87,5893
Non-polymers2,21210
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint15 kcal/mol
Surface area36070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.244, 68.924, 224.225
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 clade A/E 93TH057 HIV-1 gp120 core


Mass: 39211.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host: Homo Sapiens (human) / References: UniProt: Q0ED31*PLUS
#2: Antibody antibody VRC06 heavy chain


Mass: 25362.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): 293F / Production host: homo sapiens (human)
#3: Antibody antibody VRC06 light chain


Mass: 23014.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC8400 / Cell line (production host): 293F / 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.: 40 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG 4000, 0.2M sodium acetate, 0.1M Tris-HCl, pH 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: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 31045 / Num. obs: 29132 / % possible obs: 92.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.1 / Net I/σ(I): 13.2
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.375 / Num. unique all: 909 / Rsym value: 0.412 / % possible all: 57.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: 3SE8

3se8


Resolution: 2.6→48.72 Å / SU ML: 0.41 / σ(F): 1.36 / Phase error: 36.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2874 1454 5.01 %random
Rwork0.2475 ---
obs0.2496 29132 92.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6057 0 140 40 6237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036375
X-RAY DIFFRACTIONf_angle_d0.7468643
X-RAY DIFFRACTIONf_dihedral_angle_d12.0512341
X-RAY DIFFRACTIONf_chiral_restr0.055975
X-RAY DIFFRACTIONf_plane_restr0.0031098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69290.3862890.3281832X-RAY DIFFRACTION61
2.6929-2.80070.41421230.32632175X-RAY DIFFRACTION74
2.8007-2.92820.37971210.33262634X-RAY DIFFRACTION89
2.9282-3.08250.40271580.32272851X-RAY DIFFRACTION97
3.0825-3.27560.32951610.29882933X-RAY DIFFRACTION100
3.2756-3.52850.34671590.28482965X-RAY DIFFRACTION100
3.5285-3.88340.33111330.25753008X-RAY DIFFRACTION100
3.8834-4.4450.27251550.23833012X-RAY DIFFRACTION100
4.445-5.5990.2441570.21483045X-RAY DIFFRACTION100
5.599-48.72830.24131980.20883128X-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)
14.24493.30173.74187.44571.94625.23090.1687-0.16520.16650.351-0.3263-0.3359-0.38030.13630.06880.5872-0.04290.220.63260.05020.599412.9798-0.0493-48.5033
25.21922.29810.7286.4008-0.3545.65420.19870.0439-0.77680.0795-0.3467-1.53020.3990.47680.10030.4960.12830.11120.40050.08180.938615.4493-23.0224-50.1785
32.97230.917-4.83012.9843-4.18553.98720.962-0.60530.31641.4405-0.80320.0214-1.16720.3862-0.14461.9643-0.4811-0.0440.8179-0.06180.6914-4.8396-28.5772-26.8718
41.3027-0.3817-0.91531.3680.84962.17240.09840.71950.70081.3130.02760.2838-4.4796-1.6786-0.51893.7210.42190.26240.7751-0.03130.8607-21.1051-41.75-2.5053
50.1982-0.270.42730.5827-0.48650.94960.9532-0.58850.39022.2495-1.12310.0857-0.43530.6120.23453.5284-1.4474-0.0871.8117-0.03551.10764.9223-18.3756-9.3242
63.9081-0.6976-0.48550.83580.55570.52780.5104-0.8447-0.50870.5315-0.19-0.0814-2.21760.7919-0.1323.0644-0.7607-0.07331.20640.06850.4675-8.1357-47.38987.599
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain G and (resid 44:253 or resid 476:492)
2X-RAY DIFFRACTION2chain G and resid 254:475
3X-RAY DIFFRACTION3chain H and resid 1:131
4X-RAY DIFFRACTION4chain H and resid 132:231
5X-RAY DIFFRACTION5chain L and resid 1:103
6X-RAY DIFFRACTION6chain L and resid 104:231

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