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- PDB-1mcw: THREE-DIMENSIONAL STRUCTURE OF A HYBRID LIGHT CHAIN DIMER. PROTEI... -

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Basic information

Entry
Database: PDB / ID: 1mcw
TitleTHREE-DIMENSIONAL STRUCTURE OF A HYBRID LIGHT CHAIN DIMER. PROTEIN ENGINEERING OF A BINDING CAVITY
Components
  • IMMUNOGLOBULIN MCG (LIGHT CHAIN)
  • IMMUNOGLOBULIN WEIR (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 / adaptive immune response / Potential therapeutics for SARS / 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: 3.5 Å
AuthorsEly, K.R. / Herron, J.N. / Edmundson, A.B.
Citation
Journal: Mol.Immunol. / Year: 1990
Title: Three-dimensional structure of a hybrid light chain dimer: protein engineering of a binding cavity.
Authors: Ely, K.R. / Herron, J.N. / Edmundson, A.B.
#1: Journal: Mol.Immunol. / Year: 1985
Title: Unexpected Similarities in the Crystal Structures of the Mcg Light-Chain Dimer and its Hybrid with the Weir Protein
Authors: Ely, K.R. / Wood, M.K. / Rajan, S.S. / Hodsdon, J.M. / Abola, E.E. / Deutsch, H.F. / Edmundson, A.B.
History
DepositionMay 9, 1989Processing site: BNL
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 2.1Oct 16, 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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
W: IMMUNOGLOBULIN WEIR (LIGHT CHAIN)
M: IMMUNOGLOBULIN MCG (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)45,7442
Polymers45,7442
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-22 kcal/mol
Surface area20290 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

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Components

#1: Antibody IMMUNOGLOBULIN WEIR (LIGHT CHAIN)


Mass: 22911.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: PIR: S25758
#2: Antibody IMMUNOGLOBULIN MCG (LIGHT CHAIN)


Mass: 22833.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: PIR: S14675, UniProt: P01709*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 1.6 M / Common name: ammonium sulfate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.17 / Highest resolution: 3.5 Å
Refinement stepCycle: LAST / Highest resolution: 3.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3217 0 0 0 3217
Refinement
*PLUS
Num. reflection all: 4185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0230.03
X-RAY DIFFRACTIONp_angle_d0.0510.04
X-RAY DIFFRACTIONp_planar_d0.0290.05
X-RAY DIFFRACTIONp_chiral_restr0.0140.025

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