[English] 日本語
Yorodumi
- PDB-4zto: Fab/epitope complex structure of rabbit monoclonal antibody R53 t... -

+
Open data


ID or keywords:

Loading...

-
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 / host cell endosome membrane / actin filament organization ...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 / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more