[English] 日本語
Yorodumi
- PDB-1dee: Structure of S. aureus protein A bound to a human IgM Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dee
TitleStructure of S. aureus protein A bound to a human IgM Fab
Components
  • (IGM RF 2A2) x 2
  • IMMUNOGLOBULIN G BINDING PROTEIN A
KeywordsIMMUNE SYSTEM / FAB-IBP COMPLEX CRYSTAL STRUCTURE 2.7A RESOLUTION BINDING OUTSIDE THE ANTIGEN COMBINING SITE SUPERANTIGEN FAB VH3 SPECIFICITY
Function / homology
Function and homology information


IgG binding / extracellular region
Similarity search - Function
Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsGraille, M. / Stura, E.A. / Corper, A.L. / Sutton, B.J. / Taussig, M.J. / Charbonnier, J.B. / Silverman, G.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: structural basis for recognition of B-cell receptors and superantigen activity.
Authors: Graille, M. / Stura, E.A. / Corper, A.L. / Sutton, B.J. / Taussig, M.J. / Charbonnier, J.B. / Silverman, G.J.
History
DepositionNov 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IGM RF 2A2
B: IGM RF 2A2
C: IGM RF 2A2
D: IGM RF 2A2
E: IGM RF 2A2
F: IGM RF 2A2
G: IMMUNOGLOBULIN G BINDING PROTEIN A
H: IMMUNOGLOBULIN G BINDING PROTEIN A


Theoretical massNumber of molelcules
Total (without water)154,7408
Polymers154,7408
Non-polymers00
Water18010
1
A: IGM RF 2A2
B: IGM RF 2A2


Theoretical massNumber of molelcules
Total (without water)47,5112
Polymers47,5112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-20 kcal/mol
Surface area19040 Å2
MethodPISA
2
C: IGM RF 2A2
D: IGM RF 2A2
G: IMMUNOGLOBULIN G BINDING PROTEIN A


Theoretical massNumber of molelcules
Total (without water)53,6153
Polymers53,6153
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: IGM RF 2A2
F: IGM RF 2A2
H: IMMUNOGLOBULIN G BINDING PROTEIN A


Theoretical massNumber of molelcules
Total (without water)53,6153
Polymers53,6153
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: IGM RF 2A2
F: IGM RF 2A2


Theoretical massNumber of molelcules
Total (without water)47,5112
Polymers47,5112
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-19 kcal/mol
Surface area19040 Å2
MethodPISA
5
C: IGM RF 2A2
D: IGM RF 2A2


Theoretical massNumber of molelcules
Total (without water)47,5112
Polymers47,5112
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-19 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.520, 78.910, 163.240
Angle α, β, γ (deg.)90.00, 100.71, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody IGM RF 2A2


Mass: 23343.846 Da / Num. of mol.: 3 / Fragment: FAB LIGHT CHAIN / Source method: isolated from a natural source
Details: FAB OF THE V3-30/ VH1.9III-ENCODED 2A2 IGM RHEUMATOID FACTOR PRODUCED BY TRYPSIN CLEAVAGE OF THE IGM SECRETED BY A HYBRIDOMA CREATED FROM SYNOVIAL B CELLS OF A RHEUMATOID ARTHRITIS PATIENT
Source: (natural) Homo sapiens (human)
#2: Antibody IGM RF 2A2


Mass: 24167.008 Da / Num. of mol.: 3 / Fragment: FAB HEAVY CHAIN / Source method: isolated from a natural source
Details: FAB OF THE V3-30/ VH1.9III-ENCODED 2A2 IGM RHEUMATOID FACTOR PRODUCED BY TRYPSIN CLEAVAGE OF THE IGM SECRETED BY A HYBRIDOMA CREATED FROM SYNOVIAL B CELLS OF A RHEUMATOID ARTHRITIS PATIENT
Source: (natural) Homo sapiens (human)
#3: Antibody IMMUNOGLOBULIN G BINDING PROTEIN A


Mass: 6103.695 Da / Num. of mol.: 2 / Fragment: RECOMBINANT DOMAIN D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Staphylococcus aureus (bacteria) / References: UniProt: P02976
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPEG 5000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
221-24 %(w/w)mPEG50001reservoir
3100 mMsodium cacodylate1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceTypeIDWavelength
ROTATING ANODERIGAKU11.5418
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJul 4, 1998
MARRESEARCH2IMAGE PLATEDec 28, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 184708 / Num. obs: 46831 / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.065
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.37 / % possible all: 77
Reflection
*PLUS
% possible obs: 87 %
Reflection shell
*PLUS
% possible obs: 77 % / Mean I/σ(I) obs: 1.9

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementResolution: 2.7→10 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: The 3 amino acids at the N terminus (FNK) of chain G have been removed for the refinement as they did not fit in any electronic density. However, the same amino acids have been kept in chain ...Details: The 3 amino acids at the N terminus (FNK) of chain G have been removed for the refinement as they did not fit in any electronic density. However, the same amino acids have been kept in chain H for refinement as more electron density is observed. The side chain atoms of Lys 805 from chain H are not defined by electronic density, then we decided to remove these atoms.
RfactorNum. reflectionSelection details
Rfree0.281 2328 RANDOM
Rwork0.217 --
all0.225 46742 -
obs0.225 44414 -
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10849 0 0 10 10859
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.59

+
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