[English] 日本語
Yorodumi
- PDB-2mcg: THREE-DIMENSIONAL STRUCTURE OF A LIGHT CHAIN DIMER CRYSTALLIZED I... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mcg
TitleTHREE-DIMENSIONAL STRUCTURE OF A LIGHT CHAIN DIMER CRYSTALLIZED IN WATER. CONFORMATIONAL FLEXIBILITY OF A MOLECULE IN TWO CRYSTAL FORMS
ComponentsIMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Potential therapeutics for SARS / adaptive immune response / immune response / 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 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin lambda variable 2-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsEly, K.R. / Herron, J.N. / Edmundson, A.B.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Three-dimensional structure of a light chain dimer crystallized in water. Conformational flexibility of a molecule in two crystal forms.
Authors: Ely, K.R. / Herron, J.N. / Harker, M. / Edmundson, A.B.
#1: Journal: Mol.Immunol. / Year: 1987
Title: The Binding of Opioid Peptides to the Mcg Light Chain Dimer. Flexible Keys and Adjustable Locks
Authors: Edmundson, A.B. / Ely, K.R. / Herron, J.N. / Cheson, B.D.
#2: Journal: Progress in Immunology V / Year: 1983
Title: Three-Dimensional Structure of the Orthorhombic Form of the Mcg Bence-Jones Dimer
Authors: Ely, K.R. / Herron, J.N. / Edmundson, A.B.
#3: Journal: Biochemistry / Year: 1982
Title: Small-Angle Neutron Scattering Study of Bence-Jones Protein Mcg. Comparison of Structures in Solution and in Crystal
Authors: Schiffer, M. / Stevens, F.J. / Westholm, F.A. / Kim, S.S. / Carlson, R.D.
#4: Journal: Biochemistry / Year: 1980
Title: Marked Structural Differences of the Mcg Bence-Jones Dimer in Two Crystal Systems
Authors: Abola, E.E. / Ely, K.R. / Edmundson, A.B.
#5: Journal: Biochemistry / Year: 1978
Title: Crystal Properties as Indicators of Conformational Changes During Ligand Binding or Interconversion of Mcg Light Chain Isomers
Authors: Ely, K.R. / Firca, J.R. / Williams, K.J. / Abola, E.E. / Fenton, J.M. / Schiffer, M. / Panagiotopoulos, N.C. / Edmundson, A.B.
#6: Journal: Biochemistry / Year: 1978
Title: Interconversion of Conformational Isomers of Light Chains in the Mcg Immunoglobulins
Authors: Firca, J.R. / Ely, K.R. / Kremser, P. / Westholm, F.A. / Dorrington, K.J. / Edmundson, A.B.
#7: Journal: Sci.Am. / Year: 1977
Title: The Antibody Combining Site
Authors: Capra, J.D. / Edmundson, A.B.
#8: Journal: Antibodies in Human Diagnosis and Therapy / Year: 1977
Title: Implications of Conformational Isomerism and Rotational Allomerism to the Binding of Small Molecules by the Mcg Bence-Jones Dimer
Authors: Edmundson, A.B. / Abola, E.E. / Ely, K.R. / Firca, J.R. / Panagiotopoulos, N.C. / Schiffer, M. / Westholm, F.A.
#9: Journal: FED.PROC. / Year: 1976
Title: Conformational Isomerism,Rotational Allomerism, and Divergent Evolution in Immunoglobulin Light Chains
Authors: Edmundson, A.B. / Ely, K.R. / Abola, E.E. / Schiffer, M. / Panagiotopoulos, N. / Deutsch, H.F.
#10: Journal: Biochemistry / Year: 1975
Title: Rotational Allomerism and Divergent Evolution of Domains in Immunoglobulin Light Chains
Authors: Edmundson, A.B. / Ely, K.R. / Abola, E.E. / Schiffer, M. / Panagiotopoulos, N.
#11: Journal: Biochemistry / Year: 1974
Title: Binding of 2,4-Dinitrophenyl Compounds and Other Small Molecules to a Crystalline Lambda-Type Bence-Jones Dimer
Authors: Edmundson, A.B. / Ely, K.R. / Girling, R.L. / Abola, E.E. / Schiffer, M. / Westholm, F.A. / Fausch, M.D. / Deutsch, H.F.
#12: Journal: Progress in Immunology II / Year: 1974
Title: Structure and Binding Properties of a Lambda-Type Bence-Jones Dimer
Authors: Edmundson, A.B. / Ely, K.R. / Girling, R.L. / Abola, E.E. / Schiffer, M. / Westholm, F.A.
#13: Journal: Biochemistry / Year: 1974
Title: Primary Structure of the Mcg Lambda Chain
Authors: Fett, J.W. / Deutsch, H.F.
#14: Journal: Biochemistry / Year: 1973
Title: Preparation and Properties of a Bence-Jones Dimer with Mercury Inserted Into the Interchain Disulfide Bond
Authors: Ely, K.R. / Girling, R.L. / Schiffer, M. / Cunningham, D.E. / Edmundson, A.B.
#15: Journal: Biochemistry / Year: 1973
Title: Structure of a Lambda-Type Bence-Jones Protein at 3.5-Angstroms Resolution
Authors: Schiffer, M. / Girling, R.L. / Ely, K.R. / Edmundson, A.B.
#16: Journal: Prog.Mol.Subcell.Biol. / Year: 1973
Title: Structural Features of Immunoglobulin Light Chains
Authors: Edmundson, A.B. / Schiffer, M. / Ely, K.R. / Wood, M.K.
#17: Journal: Biochemistry / Year: 1972
Title: Structure of a Lambda-Type Bence-Jones Protein at 6-Angstroms Resolution
Authors: Edmundson, A.B. / Schiffer, M. / Ely, K.R. / Wood, M.K.
#18: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: Crystallographic Studies of an Igg Immunoglobulin and the Bence-Jones Protein from One Patient
Authors: Edmundson, A.B. / Schiffer, M. / Wood, M.K. / Hardman, K.D. / Ely, K.R. / Ainsworth, C.F.
History
DepositionMay 9, 1989Processing site: BNL
SupersessionOct 15, 1990ID: 1MCG
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Nov 20, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)
2: IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)45,6662
Polymers45,6662
Non-polymers00
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-21 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.300, 72.300, 185.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Antibody IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)


Mass: 22833.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01709
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: microdialysis / Details: solting-in
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.02 MTris-HCl1buttom
20.001 MEDTA1buttom
338 mg/mlprotein1buttom
4water1reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 7 Å / Num. obs: 12906 / Rmerge(I) obs: 5

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→7 Å / σ(I): 5 /
RfactorNum. reflection
obs0.187 12906
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 0 318 3530
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0260.03
X-RAY DIFFRACTIONp_angle_d0.0520.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0140.025
X-RAY DIFFRACTIONp_chiral_restr0.2410.15
X-RAY DIFFRACTIONp_singtor_nbd0.270.5
X-RAY DIFFRACTIONp_multtor_nbd0.40.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3870.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor6.23
X-RAY DIFFRACTIONp_staggered_tor27.915
X-RAY DIFFRACTIONp_orthonormal_tor26.720
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 7 Å / Num. reflection obs: 12906 / σ(I): 5 / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 8.76 Å2
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.3 Å

+
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