[English] 日本語
Yorodumi
- PDB-1dl7: THE STRUCTURAL BASIS OF REPERTOIRE SHIFT IN AN IMMUNE RESPONSE TO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dl7
TitleTHE STRUCTURAL BASIS OF REPERTOIRE SHIFT IN AN IMMUNE RESPONSE TO PHOSPHOCHOLINE
Components
  • PROTEIN (ANTIBODY M3C65 (HEAVY CHAIN))
  • PROTEIN (ANTIBODY M3C65 (LIGHT CHAIN))
KeywordsIMMUNE SYSTEM / SINGLE CHAIN FV / REPERTOIRE SHIFT
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / immune response / extracellular region
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
P-NITROPHENYL-PHOSPHOCHOLINE / Ig lambda-1 chain V regions MOPC 104E/RPC20/J558/S104 / Ig heavy chain V region PJ14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.35 Å
AuthorsSchumacher, M. / Brown, M.
CitationJournal: J.Exp.Med. / Year: 2000
Title: The structural basis of repertoire shift in an immune response to phosphocholine.
Authors: Brown, M. / Schumacher, M.A. / Wiens, G.D. / Brennan, R.G. / Rittenberg, M.B.
History
DepositionDec 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 2, 2013Group: Source and taxonomy
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: PROTEIN (ANTIBODY M3C65 (LIGHT CHAIN))
H: PROTEIN (ANTIBODY M3C65 (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1843
Polymers23,8792
Non-polymers3051
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-10 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.900, 35.900, 50.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO H 101
Detailsthe biological assembly is a dimer of one light chain and one heavy chain.

-
Components

#1: Antibody PROTEIN (ANTIBODY M3C65 (LIGHT CHAIN))


Mass: 11544.834 Da / Num. of mol.: 1 / Fragment: FV (SINGLE CHAIN)
Source method: isolated from a genetically manipulated source
Details: COMBINED LIGHT AND HEAVY CHAIN VIA (G4S)3 LINKER / Source: (gene. exp.) Mus musculus (house mouse) / Gene: HYBRIDOMA M3C65 / Plasmid: PET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P01724*PLUS
#2: Antibody PROTEIN (ANTIBODY M3C65 (HEAVY CHAIN))


Mass: 12333.841 Da / Num. of mol.: 1 / Fragment: FV (SINGLE CHAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: HYBRIDOMA M3C65 / Plasmid: PET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P01820*PLUS
#3: Chemical ChemComp-NCH / P-NITROPHENYL-PHOSPHOCHOLINE


Mass: 305.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N2O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: SODIUM/POTASSIUM PHOSPHATE, HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15.6 mg/mlprotein1drop
22 mMNPPC1drop
31.5 M1reservoirNaH2PO4/K2HPO4
40.1 MHEPES1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→10 Å / Num. all: 47930 / Num. obs: 8983 / % possible obs: 84 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.5
Reflection shellResolution: 2.35→2.42 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / % possible all: 52
Reflection
*PLUS
Num. measured all: 47930
Reflection shell
*PLUS
% possible obs: 47 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 1.5

-
Processing

Software
NameClassification
bioteXdata collection
bioteXdata reduction
EPMRphasing
TNTrefinement
bioteXdata scaling
RefinementResolution: 2.35→10 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.265 43 -RANDOM
Rwork0.189 ---
all0.189 47930 --
obs0.191 8983 84 %-
Refinement stepCycle: LAST / Resolution: 2.35→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 20 79 1779
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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