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- PDB-4zto: Fab/epitope complex structure of rabbit monoclonal antibody R53 t... -

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Basic information

Entry
Database: PDB / ID: 4zto
TitleFab/epitope complex structure of rabbit monoclonal antibody R53 targeting an epitope in HIV-1 gp120 C4 region
Components
  • Epitope of rabbit monoclonal antibody R53
  • RABBIT MONOCLONAL ANTIBODY R53 FAB HEAVY CHAIN
  • RABBIT MONOCLONAL ANTIBODY R53 FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / HIV-1 / Env / C4 / CD4 / monoclonal antibody
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
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 speciesOryctolagus cuniculus (rabbit)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPan, R. / Kong, X.-P.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI082274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI082676 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI065250 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI100151 United States
CitationJournal: Emerg Microbes Infect / Year: 2015
Title: Structural analysis of a novel rabbit monoclonal antibody R53 targeting an epitope in HIV-1 gp120 C4 region critical for receptor and co-receptor binding.
Authors: Pan, R. / Chen, Y. / Vaine, M. / Hu, G. / Wang, S. / Lu, S. / Kong, X.P.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: RABBIT MONOCLONAL ANTIBODY R53 FAB LIGHT CHAIN
H: RABBIT MONOCLONAL ANTIBODY R53 FAB HEAVY CHAIN
P: Epitope of rabbit monoclonal antibody R53
M: RABBIT MONOCLONAL ANTIBODY R53 FAB LIGHT CHAIN
I: RABBIT MONOCLONAL ANTIBODY R53 FAB HEAVY CHAIN
Q: Epitope of rabbit monoclonal antibody R53


Theoretical massNumber of molelcules
Total (without water)96,0096
Polymers96,0096
Non-polymers00
Water17,799988
1
L: RABBIT MONOCLONAL ANTIBODY R53 FAB LIGHT CHAIN
H: RABBIT MONOCLONAL ANTIBODY R53 FAB HEAVY CHAIN
P: Epitope of rabbit monoclonal antibody R53


Theoretical massNumber of molelcules
Total (without water)48,0053
Polymers48,0053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-37 kcal/mol
Surface area19480 Å2
MethodPISA
2
M: RABBIT MONOCLONAL ANTIBODY R53 FAB LIGHT CHAIN
I: RABBIT MONOCLONAL ANTIBODY R53 FAB HEAVY CHAIN
Q: Epitope of rabbit monoclonal antibody R53


Theoretical massNumber of molelcules
Total (without water)48,0053
Polymers48,0053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-39 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.283, 84.831, 167.237
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: Antibody RABBIT MONOCLONAL ANTIBODY R53 FAB LIGHT CHAIN


Mass: 23022.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#2: Antibody RABBIT MONOCLONAL ANTIBODY R53 FAB HEAVY CHAIN


Mass: 23322.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Homo sapiens (human)
#3: Antibody Epitope of rabbit monoclonal antibody R53


Mass: 1660.016 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 988 / 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

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 24% polyethylene glycol 6000, 0.1 M citric acid, and 0.02% NaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 48392 / % possible obs: 99.1 % / Redundancy: 6.5 % / Rsym value: 0.165 / Net I/σ(I): 18
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.483 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
MOLREPphasing
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JO1

4jo1


Resolution: 2.3→44.143 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.28 / Phase error: 19.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 2299 5.04 %
Rwork0.167 --
obs0.1698 45616 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→44.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6632 0 0 988 7620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086806
X-RAY DIFFRACTIONf_angle_d1.0739305
X-RAY DIFFRACTIONf_dihedral_angle_d13.0512359
X-RAY DIFFRACTIONf_chiral_restr0.0391096
X-RAY DIFFRACTIONf_plane_restr0.0051181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.30461200.2042567X-RAY DIFFRACTION94
2.35-2.40470.28771640.20112566X-RAY DIFFRACTION95
2.4047-2.46480.29291430.20782646X-RAY DIFFRACTION97
2.4648-2.53140.25391730.2012607X-RAY DIFFRACTION97
2.5314-2.60590.28941330.1922662X-RAY DIFFRACTION98
2.6059-2.690.26351430.18692678X-RAY DIFFRACTION98
2.69-2.78620.25361530.17482713X-RAY DIFFRACTION99
2.7862-2.89770.23951410.17772706X-RAY DIFFRACTION99
2.8977-3.02950.22071280.17382749X-RAY DIFFRACTION99
3.0295-3.18920.20031360.16332723X-RAY DIFFRACTION99
3.1892-3.3890.19441530.15872723X-RAY DIFFRACTION100
3.389-3.65050.20481450.15582733X-RAY DIFFRACTION99
3.6505-4.01770.19391390.14882789X-RAY DIFFRACTION99
4.0177-4.59850.18191350.13522747X-RAY DIFFRACTION99
4.5985-5.79160.19091410.14112816X-RAY DIFFRACTION99
5.7916-44.15110.21041520.17992892X-RAY DIFFRACTION97

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