[English] 日本語
Yorodumi
- PDB-2aj3: Crystal Structure of a Cross-Reactive HIV-1 Neutralizing CD4-Bind... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2aj3
TitleCrystal Structure of a Cross-Reactive HIV-1 Neutralizing CD4-Binding Site Antibody Fab m18
Components
  • Fab m18, Heavy Chain
  • Fab m18, Light Chain
KeywordsIMMUNE SYSTEM / HIV / antibody / Fab / CD4-binding / immunoglobulin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsPrabakaran, P. / Gan, J. / Wu, Y.Q. / Zhang, M.Y. / Dimitrov, D.S. / Ji, X.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural mimicry of CD4 by a cross-reactive HIV-1 neutralizing antibody with CDR-H2 and H3 containing unique motifs.
Authors: Prabakaran, P. / Gan, J. / Wu, Y.Q. / Zhang, M.Y. / Dimitrov, D.S. / Ji, X.
History
DepositionAug 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The sequences of the proteins were not deposited into any sequence database. The sequence ...SEQUENCE The sequences of the proteins were not deposited into any sequence database. The sequence of FAB M18 was selected from a human phage display library (Immunol. Methods, 283(1-2):17-25, Dec. 2003). The constant domains of the heavy chains B, D and F have the same sequence as all human IGG1 antibodies.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fab m18, Light Chain
B: Fab m18, Heavy Chain
C: Fab m18, Light Chain
D: Fab m18, Heavy Chain
E: Fab m18, Light Chain
F: Fab m18, Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,8819
Polymers143,5936
Non-polymers2883
Water8,989499
1
A: Fab m18, Light Chain
B: Fab m18, Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9603
Polymers47,8642
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-35 kcal/mol
Surface area19890 Å2
MethodPISA
2
C: Fab m18, Light Chain
D: Fab m18, Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9603
Polymers47,8642
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-38 kcal/mol
Surface area20120 Å2
MethodPISA
3
E: Fab m18, Light Chain
F: Fab m18, Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9603
Polymers47,8642
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-38 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.599, 82.620, 187.204
Angle α, β, γ (deg.)90.00, 95.27, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody Fab m18, Light Chain


Mass: 23441.111 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Fab / Plasmid: pComb3X / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: Q6PIH7
#2: Antibody Fab m18, Heavy Chain


Mass: 24423.268 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Fab / Plasmid: pComb3X / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: Q6GMX1
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 100 mM CHES, 20% (w/v) PEG-8000, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 17, 2004 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→29.25 Å / Num. all: 81882 / Num. obs: 81882 / % possible obs: 85.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.89 / Num. unique all: 6545 / % possible all: 70

-
Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HZH

1hzh


Resolution: 2.03→29.25 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 351921.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 4133 5 %RANDOM
Rwork0.225 ---
all0.227 81882 --
obs0.227 81882 85.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.8949 Å2 / ksol: 0.331035 e/Å3
Displacement parametersBiso mean: 32.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.81 Å20 Å25 Å2
2--3.02 Å20 Å2
3----7.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-30 Å
Luzzati sigma a0.51 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.03→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9983 0 15 499 10497
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_improper_angle_d1.02
LS refinement shellResolution: 2.03→2.1 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.388 341 5.1 %
Rwork0.404 6283 -
obs-6624 70 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

+
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