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- PDB-1zvo: Semi-extended solution structure of human myeloma immunoglobulin ... -

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Basic information

Entry
Database: PDB / ID: 1zvo
TitleSemi-extended solution structure of human myeloma immunoglobulin D determined by constrained X-ray scattering
Components
  • Immunoglobulin delta heavy chain
  • myeloma immunoglobulin D lambda
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / ANTIBODY
Function / homology
Function and homology information


monocyte activation / opsonization / regulation of complement activation / positive regulation of interleukin-1 production / peptide cross-linking / CD22 mediated BCR regulation / immunoglobulin complex / complement activation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation ...monocyte activation / opsonization / regulation of complement activation / positive regulation of interleukin-1 production / peptide cross-linking / 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 / negative regulation of inflammatory response to antigenic stimulus / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / receptor-mediated endocytosis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of interleukin-1 beta production / 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 / positive regulation of tumor necrosis factor production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / blood microparticle / immune response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin / Immunoglobulin 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 subtype / Immunoglobulin / Immunoglobulin C-Type ...Immunoglobulin / Immunoglobulin 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 subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin lambda variable 1-47 / Immunoglobulin delta heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION SCATTERING / SYNCHROTRON
AuthorsSun, Z. / Almogren, A. / Furtado, P.B. / Chowdhury, B. / Kerr, M.A. / Perkins, S.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Semi-extended Solution Structure of Human Myeloma Immunoglobulin D Determined by Constrained X-ray Scattering.
Authors: Sun, Z. / Almogren, A. / Furtado, P.B. / Chowdhury, B. / Kerr, M.A. / Perkins, S.J.
History
DepositionJun 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_nat.common_name ..._entity.pdbx_description / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: myeloma immunoglobulin D lambda
B: myeloma immunoglobulin D lambda
C: Immunoglobulin delta heavy chain
D: Immunoglobulin delta heavy chain


Theoretical massNumber of molelcules
Total (without water)158,4934
Polymers158,4934
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody myeloma immunoglobulin D lambda / Coordinate model: Cα atoms only


Mass: 22962.377 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Myeloma / Source: (natural) Homo sapiens (human) / References: UniProt: P01700*PLUS
#2: Antibody Immunoglobulin delta heavy chain / Immunoglobulin delta heavy chain WAH / Coordinate model: Cα atoms only


Mass: 56284.090 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Myeloma / Source: (natural) Homo sapiens (human) / References: UniProt: P0DOX3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Mar 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Soln scatterType: x-ray / Buffer name: 12.5 MM NA PHOSPHATE, 140 MM NACL / Conc. range: 0.30-0.89 / Data analysis software list: SCTPL7, GNOM / Data reduction software list: MULTICCD / Detector type: FRELON CCD CAMERA / Max mean cross sectional radii gyration: 1.24 nm / Max mean cross sectional radii gyration esd: 0.15 nm / Mean guiner radius: 6.94 nm / Mean guiner radius esd: 0.12 nm / Min mean cross sectional radii gyration: 1.93 nm / Min mean cross sectional radii gyration esd: 0.04 nm / Num. of time frames: 1 / Protein length: 1 / Sample pH: 7.2 / Source beamline: ID02 / Source class: Y / Source type: ESRF BEAMLINE ID02 / Temperature: 288 K

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Processing

SoftwareName: Insight II / Version: II 98.0 / Classification: model building
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 0 0 1452
Soln scatter modelMethod: CONSTRAINED SCATTERING FITTING OF HOMOLOGY MODELS
Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG AND RXS-1 VALUES IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN ...Conformer selection criteria: THE MODELLED SCATTERING CURVES WERE ASSESSED BY CALCULATION OF THE RG AND RXS-1 VALUES IN THE SAME Q RANGES USED IN THE EXPERIMENTAL GUINIER FITS. MODELS WERE THEN RANKED USING A GOODNESS-OF-FIT R-FACTOR DEFINED BY ANALOGY WITH PROTEIN CRYSTALLOGRAPHY
Details: HOMOLOGY MODELS WERE BUILT FOR THE FAB AND FC FRAGMENTS BY TRIAL AND ERROR CONSTRAINED MODELLING. THE POSITIONS OF THE FRAGMENTS WERE DETERMINED BY AN APPROACH THAT COMBINED RANDOMISED HINGE ...Details: HOMOLOGY MODELS WERE BUILT FOR THE FAB AND FC FRAGMENTS BY TRIAL AND ERROR CONSTRAINED MODELLING. THE POSITIONS OF THE FRAGMENTS WERE DETERMINED BY AN APPROACH THAT COMBINED RANDOMISED HINGE PEPTIDE STRUCTURES PRODUCED BY MOLECULAR DYNAMICS SIMULATIONS WITH CURVE-FITTING TO EXPERIMENTAL X-RAY SOLUTION SCATTERING DATA. A SINGLE ARRANGEMENT OF THE FAB AND FC FRAGMENTS IS PRESENTED, WHICH IS REPRESENTATIVE OF A FAMILY OF STRUCTURES THAT FIT THE SCATTERING DATA. MORE DETAILS ON THE MODELLING STRATEGY ARE CONTAINED IN THE PRIMARY REFERENCE.
Num. of conformers calculated: 8500 / Num. of conformers submitted: 1 / Representative conformer: 1 / Software author list: ACCELRYS
Software list: INSIGHT II, HOMOLOGY, DISCOVERY, BIOPOLYMER, DELPHI, O, SCTPL7, GNOM

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