[English] 日本語
Yorodumi
- PDB-1wtl: COMPARISON OF CRYSTAL STRUCTURES OF TWO HOMOLOGOUS PROTEINS: STRU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wtl
TitleCOMPARISON OF CRYSTAL STRUCTURES OF TWO HOMOLOGOUS PROTEINS: STRUCTURAL ORIGIN OF ALTERED DOMAIN INTERACTIONS IN IMMUNOGLOBULIN LIGHT CHAIN DIMERS
ComponentsBENCE-JONES PROTEIN MCG (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


immunoglobulin production / regulation of complement activation / CD22 mediated BCR regulation / immunoglobulin complex / complement activation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / leukocyte migration / Fc-gamma receptor signaling pathway involved in phagocytosis ...immunoglobulin production / regulation of complement activation / CD22 mediated BCR regulation / immunoglobulin complex / complement activation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / leukocyte migration / Fc-gamma receptor signaling pathway involved in phagocytosis / Fc-epsilon receptor signaling pathway / FCGR activation / regulation of immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / receptor-mediated endocytosis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
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 / Immunoglobulins / Immunoglobulin-like fold ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa variable 1D-33 / Immunoglobulin kappa variable 1D-33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsHuang, D.B. / Chang, C.H. / Schiffer, M.
Citation
Journal: Biochemistry / Year: 1994
Title: Comparison of crystal structures of two homologous proteins: structural origin of altered domain interactions in immunoglobulin light-chain dimers.
Authors: Huang, D.B. / Chang, C.H. / Ainsworth, C. / Brunger, A.T. / Eulitz, M. / Solomon, A. / Stevens, F.J. / Schiffer, M.
#1: Journal: J.Mol.Biol. / Year: 1981
Title: Characterization and Preliminary Crystallographic Data on the Vl-Related Fragment of the Human Ki Bence-Jones Protein Wat
Authors: Stevens, F.J. / Westholm, F.A. / Panagiotopoulos, N. / Schiffer, M. / Popp, R.A. / Solomon, A.
#2: Journal: Biochemistry / Year: 1975
Title: The Molecular Structure of a Dimer Composed of the Variable Portions of the Bence-Jones Protein Rei Refined at 2.0 Angstroms Resolution
Authors: Schiffer, M. / Epp, O. / Lattman, E.E. / Schiffer, M. / Huber, R. / Palm, W.
History
DepositionJun 8, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BENCE-JONES PROTEIN MCG (LIGHT CHAIN)
B: BENCE-JONES PROTEIN MCG (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)23,4902
Polymers23,4902
Non-polymers00
Water3,531196
1
A: BENCE-JONES PROTEIN MCG (LIGHT CHAIN)
B: BENCE-JONES PROTEIN MCG (LIGHT CHAIN)

A: BENCE-JONES PROTEIN MCG (LIGHT CHAIN)
B: BENCE-JONES PROTEIN MCG (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,9804
Polymers46,9804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)82.250, 82.250, 61.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Atom site foot note1: CIS PROLINE - PRO A 8 / 2: CIS PROLINE - PRO A 95 / 3: CIS PROLINE - PRO B 8 / 4: CIS PROLINE - PRO B 95
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.58747, -0.30138, 0.75103), (-0.33404, -0.755, -0.56426), (0.73703, -0.58232, 0.34285)
Vector: -15.707, 72.652, 39.204)

-
Components

#1: Antibody BENCE-JONES PROTEIN MCG (LIGHT CHAIN)


Mass: 11745.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P80362, UniProt: P01593*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: microdialysis
Components of the solutions
*PLUS
Conc.: 20 % / Common name: dextran

-
Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→10 Å / σ(F): 3 /
RfactorNum. reflection
obs0.157 10320
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1650 0 0 196 1846
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0420.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.741
X-RAY DIFFRACTIONp_mcangle_it1.291.5
X-RAY DIFFRACTIONp_scbond_it1.181.5
X-RAY DIFFRACTIONp_scangle_it1.82
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.1770.15
X-RAY DIFFRACTIONp_singtor_nbd0.1980.3
X-RAY DIFFRACTIONp_multtor_nbd0.2360.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2090.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.73
X-RAY DIFFRACTIONp_staggered_tor23.513
X-RAY DIFFRACTIONp_orthonormal_tor18.120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ/X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.157
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://pdbjlvh1.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