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- PDB-4xmk: Crystal structure of Fab of HIV-1 gp120 V3-specific human monoclo... -

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Basic information

Entry
Database: PDB / ID: 4xmk
TitleCrystal structure of Fab of HIV-1 gp120 V3-specific human monoclonal antibody 2424 in complex with JR-FL V3 peptide
Components
  • HIV-1 JR-FL gp120 V3 peptide
  • Heavy chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
  • Light chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
Keywordsimmune system/viral protein / HIV-1 gp120 / monoclonal antibody / immune system-viral protein complex
Function / homology
Function and homology information


Dectin-2 family / 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 ...Dectin-2 family / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane / identical protein binding
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.179 Å
AuthorsKong, X.-P. / Pan, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI082274 United States
CitationJournal: J.Virol. / Year: 2015
Title: Functional and Structural Characterization of Human V3-Specific Monoclonal Antibody 2424 with Neutralizing Activity against HIV-1 JRFL.
Authors: Kumar, R. / Pan, R. / Upadhyay, C. / Mayr, L. / Cohen, S. / Wang, X.H. / Balasubramanian, P. / Nadas, A. / Seaman, M.S. / Zolla-Pazner, S. / Gorny, M.K. / Kong, X.P. / Hioe, C.E.
History
DepositionJan 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2May 31, 2017Group: Other
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Light chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
H: Heavy chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
P: HIV-1 JR-FL gp120 V3 peptide
M: Light chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
I: Heavy chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
Q: HIV-1 JR-FL gp120 V3 peptide
N: Light chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
J: Heavy chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
R: HIV-1 JR-FL gp120 V3 peptide


Theoretical massNumber of molelcules
Total (without water)145,3899
Polymers145,3899
Non-polymers00
Water0
1
L: Light chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
H: Heavy chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
P: HIV-1 JR-FL gp120 V3 peptide


Theoretical massNumber of molelcules
Total (without water)48,4633
Polymers48,4633
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-28 kcal/mol
Surface area19000 Å2
MethodPISA
2
M: Light chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
I: Heavy chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
Q: HIV-1 JR-FL gp120 V3 peptide


Theoretical massNumber of molelcules
Total (without water)48,4633
Polymers48,4633
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-28 kcal/mol
Surface area19120 Å2
MethodPISA
3
N: Light chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
J: Heavy chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424
R: HIV-1 JR-FL gp120 V3 peptide


Theoretical massNumber of molelcules
Total (without water)48,4633
Polymers48,4633
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-28 kcal/mol
Surface area18780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.952, 122.254, 140.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
33

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'L' and (resseq 2:210 )
211chain 'M' and (resseq 2:210 )
311chain 'N' and (resseq 2:210 )
112chain 'H' and (resseq 1:126 or resseq 135:213 )
212chain 'I' and (resseq 1:126 or resseq 135:213 )
312chain 'J' and (resseq 1:126 or resseq 135:213 )
113chain 'P' and (resseq 301:320 )
213chain 'Q' and (resseq 301:320 )
313chain 'R' and (resseq 301:320 )

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Light chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424


Mass: 23533.193 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Heavy chain of HIV-1 gp120 V3-specific human monoclonal antibody 2424


Mass: 23696.426 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide HIV-1 JR-FL gp120 V3 peptide


Mass: 1233.419 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P05877*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 4000, Li2SO4, Tris, glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.179→50 Å / Num. obs: 53260 / % possible obs: 99.9 % / Redundancy: 14.7 % / Net I/σ(I): 11.6
Reflection shellResolution: 3.18→3.37 Å / Redundancy: 14.6 % / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementResolution: 3.179→48.282 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2832 2657 4.99 %
Rwork0.2248 --
obs0.2277 53260 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.179→48.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10085 0 0 0 10085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910337
X-RAY DIFFRACTIONf_angle_d1.18314040
X-RAY DIFFRACTIONf_dihedral_angle_d15.9673694
X-RAY DIFFRACTIONf_chiral_restr0.0441554
X-RAY DIFFRACTIONf_plane_restr0.0061813
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11L1646X-RAY DIFFRACTIONPOSITIONAL
12M1646X-RAY DIFFRACTIONPOSITIONAL0.069
13N1635X-RAY DIFFRACTIONPOSITIONAL0.053
21H1619X-RAY DIFFRACTIONPOSITIONAL
22I1619X-RAY DIFFRACTIONPOSITIONAL0.08
23J1619X-RAY DIFFRACTIONPOSITIONAL0.05
31P87X-RAY DIFFRACTIONPOSITIONAL
32Q87X-RAY DIFFRACTIONPOSITIONAL0.031
33R87X-RAY DIFFRACTIONPOSITIONAL0.034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1791-3.23690.38821410.31882660X-RAY DIFFRACTION99
3.2369-3.29910.37871400.31022645X-RAY DIFFRACTION100
3.2991-3.36650.32181440.30152665X-RAY DIFFRACTION100
3.3665-3.43960.39811370.2922668X-RAY DIFFRACTION100
3.4396-3.51960.36241410.29532694X-RAY DIFFRACTION100
3.5196-3.60760.37451400.27572667X-RAY DIFFRACTION100
3.6076-3.70510.32931370.2642628X-RAY DIFFRACTION100
3.7051-3.81410.26781420.23922701X-RAY DIFFRACTION100
3.8141-3.93720.31191360.24142634X-RAY DIFFRACTION100
3.9372-4.07780.2951430.24532681X-RAY DIFFRACTION100
4.0778-4.2410.30951370.22982654X-RAY DIFFRACTION100
4.241-4.43390.29531420.21232650X-RAY DIFFRACTION100
4.4339-4.66750.25621430.20622657X-RAY DIFFRACTION100
4.6675-4.95960.25741410.19842649X-RAY DIFFRACTION100
4.9596-5.34210.26861380.18452700X-RAY DIFFRACTION100
5.3421-5.87890.23021380.19282654X-RAY DIFFRACTION100
5.8789-6.72760.23031430.22671X-RAY DIFFRACTION100
6.7276-8.46860.2241340.18592663X-RAY DIFFRACTION100
8.4686-48.28720.22271400.17952662X-RAY DIFFRACTION100

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