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- PDB-2fb4: DIR PRIMAERSTRUKTUR DES KRISTALLISIERBAREN MONOKLONALEN IMMUNOGLO... -

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Basic information

Entry
Database: PDB / ID: 2fb4
TitleDIR PRIMAERSTRUKTUR DES KRISTALLISIERBAREN MONOKLONALEN IMMUNOGLOBULINS IGG1 KOL. II. AMINOSAEURESEQUENZ DER L-KETTE, LAMBDA-TYP, SUBGRUPPE I (GERMAN)
Components
  • IGG1-LAMBDA KOL FAB (HEAVY CHAIN)
  • IGG1-LAMBDA KOL FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / immunoglobulin complex / Initial triggering of complement ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / immunoglobulin complex / Initial triggering of complement / immunoglobulin mediated immune response / 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 / B cell receptor signaling pathway / 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 / blood microparticle / adaptive immune response / Potential therapeutics for SARS / 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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / 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 heavy variable 3-33 / Immunoglobulin lambda constant 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsMarquart, M. / Huber, R.
Citation
Journal: Biol.Chem.Hoppe-Seyler / Year: 1989
Title: The primary structure of crystallizable monoclonal immunoglobulin IgG1 Kol. II. Amino acid sequence of the L-chain, gamma-type, subgroup I
Authors: Kratzin, H.D. / Palm, W. / Stangel, M. / Schmidt, W.E. / Friedrich, J. / Hilschmann, N.
#1: Journal: Immunol.Today / Year: 1982
Title: The Three-Dimensional Structure of Antibodies
Authors: Marquart, M. / Deisenhofer, J.
#2: Journal: J.Mol.Biol. / Year: 1980
Title: Crystallographic Refinement and Atomic Models of the Intact Immunoglobulin Molecule Kol and its Antigen-Binding Fragment at 3.0 Angstroms and 1.9 Angstroms Resolution
Authors: Marquart, M. / Deisenhofer, J. / Huber, R. / Palm, W.
#3: Journal: J.Mol.Biol. / Year: 1978
Title: Crystal Structure of the Human Fab Fragment Kol and its Comparison with the Intact Kol Molecule
Authors: Matsushima, M. / Marquart, M. / Jones, T.A. / Colman, P.M. / Bartels, K. / Huber, R.
#4: Journal: Nature / Year: 1976
Title: Crystallographic Structure Studies of an Igg Molecule and an Fc Fragment
Authors: Huber, R. / Deisenhofer, J. / Colman, P.M. / Matsushima, M. / Palm, W.
#5: Journal: J.Mol.Biol. / Year: 1976
Title: Structure of the Human Antibody Molecule Kol (Immunoglobulin G1). An Electron Density Map at 5 Angstroms Resolution
Authors: Colman, P.M. / Deisenhofer, J. / Huber, R. / Palm, W.
History
DepositionApr 18, 1989Processing site: BNL
SupersessionJul 12, 1989ID: 1FB4
Revision 1.0Jul 12, 1989Provider: 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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 / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: IGG1-LAMBDA KOL FAB (LIGHT CHAIN)
H: IGG1-LAMBDA KOL FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,1422
Polymers47,1422
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-26 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.300, 138.900, 40.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES L 143, H 152, H 154 ARE CIS-PROLINES.
2: THESE ATOMS WERE NOT FOUND IN THE ELECTRON DENSITY MAP. THEIR COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA.

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Components

#1: Antibody IGG1-LAMBDA KOL FAB (LIGHT CHAIN)


Mass: 22817.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P0CG04*PLUS
#2: Antibody IGG1-LAMBDA KOL FAB (HEAVY CHAIN)


Mass: 24325.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01772
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal grow
*PLUS
Method: unknown

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 1.9→6 Å / Rfactor Rwork: 0.189
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 0 105 3417
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS

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