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- PDB-4j6r: Crystal structure of broadly and potently neutralizing antibody V... -

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Basic information

Entry
Database: PDB / ID: 4j6r
TitleCrystal structure of broadly and potently neutralizing antibody VRC23 in complex with HIV-1 gp120
Components
  • Envelope glycoprotein gp160
  • HEAVY CHAIN OF ANTIBODY VRC23
  • LIGHT CHAIN OF ANTIBODY VRC23
Keywordsviral protein/immune system / HIV / GP120 / CD4-binding site / VRC23 / NEUTRALIZATION / VACCINE / Antibody / envelope protein / immune system / viral protein-immune system complex
Function / homology
Function and homology information


host cell endosome membrane / membrane => GO:0016020 / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / 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 ...HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / 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
(R,R)-2,3-BUTANEDIOL / Env polyprotein
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsZhou, T. / Moquin, 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 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Envelope glycoprotein gp160
H: HEAVY CHAIN OF ANTIBODY VRC23
L: LIGHT CHAIN OF ANTIBODY VRC23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,60432
Polymers87,2723
Non-polymers3,33229
Water18,3751020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.044, 68.692, 214.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody HEAVY CHAIN OF ANTIBODY VRC23


Mass: 24445.516 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 LIGHT CHAIN OF ANTIBODY VRC23


Mass: 22846.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: HOMO SAPIENS (human)

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Protein / Sugars , 2 types, 10 molecules G

#1: Protein Envelope glycoprotein gp160


Mass: 39980.078 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: Q8J581*PLUS
#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.: 9
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

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Non-polymers , 6 types, 1040 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1020 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10.5 % PEG 4000, 4 % MPD, 100 mM Tris/HCl, 200 mM CaCl2 , 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2012
RadiationMonochromator: APS 22ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. all: 113960 / Num. obs: 108035 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 21.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SE9

3se9


Resolution: 1.64→23.173 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 19.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1976 5396 5 %Radom
Rwork0.1635 ---
obs0.1652 107945 94.57 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→23.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6015 0 210 1020 7245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056366
X-RAY DIFFRACTIONf_angle_d1.018614
X-RAY DIFFRACTIONf_dihedral_angle_d13.0472315
X-RAY DIFFRACTIONf_chiral_restr0.06975
X-RAY DIFFRACTIONf_plane_restr0.0051083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.635-1.65360.30681710.25612964X-RAY DIFFRACTION84
1.6536-1.67310.25681710.24053285X-RAY DIFFRACTION92
1.6731-1.69350.2711800.22853364X-RAY DIFFRACTION94
1.6935-1.71490.2531970.21813374X-RAY DIFFRACTION94
1.7149-1.73740.26921780.21853374X-RAY DIFFRACTION95
1.7374-1.76120.24251980.21593434X-RAY DIFFRACTION96
1.7612-1.78640.24131860.21083392X-RAY DIFFRACTION96
1.7864-1.8130.22951840.20653474X-RAY DIFFRACTION96
1.813-1.84140.25021690.19843435X-RAY DIFFRACTION96
1.8414-1.87150.23911690.18873431X-RAY DIFFRACTION96
1.8715-1.90380.23871830.18823456X-RAY DIFFRACTION97
1.9038-1.93840.22721990.18213450X-RAY DIFFRACTION96
1.9384-1.97570.23861590.18173482X-RAY DIFFRACTION97
1.9757-2.0160.21821710.1813475X-RAY DIFFRACTION96
2.016-2.05980.21411940.17033386X-RAY DIFFRACTION95
2.0598-2.10770.19421880.16813431X-RAY DIFFRACTION96
2.1077-2.16030.24781580.16733452X-RAY DIFFRACTION95
2.1603-2.21870.21261750.16853440X-RAY DIFFRACTION95
2.2187-2.28390.20881590.1633429X-RAY DIFFRACTION95
2.2839-2.35760.21931720.16163426X-RAY DIFFRACTION95
2.3576-2.44170.19242110.1633362X-RAY DIFFRACTION94
2.4417-2.53940.19991750.15593389X-RAY DIFFRACTION94
2.5394-2.65480.1951820.15683399X-RAY DIFFRACTION94
2.6548-2.79460.20491740.16283369X-RAY DIFFRACTION93
2.7946-2.96930.19111740.16043388X-RAY DIFFRACTION93
2.9693-3.1980.18211830.1493388X-RAY DIFFRACTION93
3.198-3.51890.16561650.14493389X-RAY DIFFRACTION92
3.5189-4.02580.16021810.13923480X-RAY DIFFRACTION94
4.0258-5.06330.16772060.13163659X-RAY DIFFRACTION98
5.0633-23.17520.20221840.18763772X-RAY DIFFRACTION96
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)
13.2292-0.89981.59644.60430.53414.4432-0.1028-0.08340.447-0.3049-0.02410.1237-0.4392-0.1190.090.26260.01090.00020.1806-0.04320.2475-12.3952.33945.4738
22.76490.15980.63052.51020.95063.4674-0.0083-0.4071-0.09250.2987-0.06070.26850.3393-0.40390.0320.2225-0.00690.05080.23130.00070.177-15.8331-20.778347.0053
31.4552-0.489-0.20042.86130.20321.9477-0.0185-0.12110.05570.0956-0.0376-0.09630.0220.1220.050.1341-0.0037-0.00320.1510.00950.11152.4804-26.534427.0636
42.87770.5309-2.12862.5719-1.39876.6984-0.08780.1479-0.1208-0.09320.0811-0.14590.0880.1463-0.00420.11180.0242-0.00360.1119-0.01530.220519.0419-42.3530.505
50.991-0.4422-0.55492.2018-0.18223.7210.05860.08410.0348-0.1116-0.0666-0.03360.0559-0.08210.01420.12480.0321-0.02010.11980.00560.1504-7.0249-19.31327.2084
61.1927-0.80870.23936.312-0.55351.76260.03740.1102-0.2666-0.1460.0276-0.05040.2124-0.0666-0.06520.1316-0.00570.01850.1652-0.02690.19756.8055-47.7853-8.101
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 1:113
4X-RAY DIFFRACTION4chain H and resid 114:217
5X-RAY DIFFRACTION5chain L and resid 1:108
6X-RAY DIFFRACTION6chain L and resid 109:215

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