[English] 日本語
Yorodumi
- PDB-2cd0: STRUCTURE OF HUMAN LAMBDA-6 LIGHT CHAIN DIMER WIL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cd0
TitleSTRUCTURE OF HUMAN LAMBDA-6 LIGHT CHAIN DIMER WIL
ComponentsPROTEIN (BENCE-JONES PROTEIN WIL, A VARIABLE DOMAIN FROM LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / BENCE-JONES PROTEIN / LAMBDA-6
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / 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 / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / antigen binding / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / 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 / immune response / extracellular space / 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 lambda variable 6-57
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPokkuluri, P.R. / Solomon, A. / Weiss, D.T. / Stevens, F.J. / Schiffer, M.
CitationJournal: Amyloid / Year: 1999
Title: Tertiary structure of human lambda 6 light chains.
Authors: Pokkuluri, P.R. / Solomon, A. / Weiss, D.T. / Stevens, F.J. / Schiffer, M.
History
DepositionMar 8, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (BENCE-JONES PROTEIN WIL, A VARIABLE DOMAIN FROM LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN)
B: PROTEIN (BENCE-JONES PROTEIN WIL, A VARIABLE DOMAIN FROM LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)24,0042
Polymers24,0042
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.900, 147.900, 46.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsTHE BIOLOGICALLY ACTIVE MOLECULE IS A HOMODIMER. THE ASYMMETRIC UNIT CONTAINS BOTH MONOMERS, CHAINS A AND B. BOTH MONOMERS REFINED INDEPENDENTLY.

-
Components

#1: Antibody PROTEIN (BENCE-JONES PROTEIN WIL, A VARIABLE DOMAIN FROM LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN)


Mass: 12001.915 Da / Num. of mol.: 2 / Fragment: VARIABLE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5LAMBDA / References: GenBank: 587410, UniProt: P01721*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.5 %
Description: CONSTANT DOMAINS WERE ALSO REMOVED FROM MCG MODEL PRIOR TO MOLECULAR REPLACEMENT.
Crystal growpH: 5.6
Details: 1.8M AMMONIUM SULPHATE, 0.1 M SODIUM CITRATE PH 5.6, 0.01 M CADMIUM CHLORIDE
Crystal grow
*PLUS
Method: vapor diffusion / PH range low: 8.5 / PH range high: 4.6
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1ammonium sulfate1reservoir
2PEG60001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 21478 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 21.8 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 48
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 9 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 19 / % possible all: 96.4
Reflection shell
*PLUS
% possible obs: 96.4 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MCG (1DCL): USED ONLY VL DIMER WITH CDR LOOPS DELETED.
Resolution: 1.8→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 1379583.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.351 1689 9.8 %RANDOM
Rwork0.289 ---
obs-17271 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65 Å2 / ksol: 0.49 e/Å3
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å2-2.21 Å20 Å2
2---2.28 Å20 Å2
3---4.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 0 112 1724
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.78
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.021.5
X-RAY DIFFRACTIONx_mcangle_it1.742
X-RAY DIFFRACTIONx_scbond_it1.162
X-RAY DIFFRACTIONx_scangle_it1.682.5
LS refinement shellResolution: 1.8→1.82 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 33
RfactorNum. reflection% reflection
Rfree0.41 58 11.9 %
Rwork0.363 431 -
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

+
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