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- PDB-1cbv: AN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE THREE-D... -

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Basic information

Entry
Database: PDB / ID: 1cbv
TitleAN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF THE UNLIGANDED FAB AND A DEOXYNUCLEOTIDE-FAB COMPLEX
Components
  • DNA (5'-D(*TP*TP*T)-3')
  • PROTEIN (FAB (BV04-01) AUTOANTIBODY-HEAVY CHAIN)
  • PROTEIN (FAB (BV04-01) AUTOANTIBODY-LIGHT CHAIN)
KeywordsIMMUNE SYSTEM/DNA / PROTEIN-DNA COMPLEX / SINGLE STRAND / IMMUNE SYSTEM-DNA COMPLEX
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / positive regulation of immune response / extracellular space / extracellular region / metal ion binding / 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 subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / If kappa light chain / Immunoglobulin heavy constant gamma 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.66 Å
AuthorsHerron, J.N. / He, X.M. / Ballard, D.W. / Blier, P.R. / Pace, P.E. / Bothwell, A.L.M. / Voss Junior, E.W. / Edmundson, A.B.
Citation
Journal: Proteins / Year: 1991
Title: An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex.
Authors: Herron, J.N. / He, X.M. / Ballard, D.W. / Blier, P.R. / Pace, P.E. / Bothwell, A.L. / Voss Jr., E.W. / Edmundson, A.B.
#1: Journal: Mol.Immunol. / Year: 1985
Title: Crystallographic Characterization of the FAB Fragment of a Monoclonal Anti-SS- DNA Antibody
Authors: Gibson, A.L. / Herron, J.N. / Ballard, D.W. / Voss, E.W. / He, X.M. / Patrick, V.A. / Edmundson, A.B.
History
DepositionMar 16, 1993Processing site: NDB
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2014Group: Source and taxonomy
Revision 1.4Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA (5'-D(*TP*TP*T)-3')
L: PROTEIN (FAB (BV04-01) AUTOANTIBODY-LIGHT CHAIN)
H: PROTEIN (FAB (BV04-01) AUTOANTIBODY-HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)48,5313
Polymers48,5313
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.500, 99.200, 36.600
Angle α, β, γ (deg.)90.00, 95.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain DNA (5'-D(*TP*TP*T)-3')


Mass: 867.621 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Antibody PROTEIN (FAB (BV04-01) AUTOANTIBODY-LIGHT CHAIN)


Mass: 24109.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: A2NHM3*PLUS
#3: Antibody PROTEIN (FAB (BV04-01) AUTOANTIBODY-HEAVY CHAIN)


Mass: 23553.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01867*PLUS
Compound detailsTURNS L2, L4, AND L10 CONTAIN ONLY 3 RESIDUES.
Has protein modificationY
Sequence detailsTHE PROTEIN WAS SEQUENCED BY D. W. BALLARD, P. R. BLIER, P. E. PACE, AND A. L. M. BOTHWELL. SEE ...THE PROTEIN WAS SEQUENCED BY D. W. BALLARD, P. R. BLIER, P. E. PACE, AND A. L. M. BOTHWELL. SEE REFERENCE 1 ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7.6 / Method: unknown
Components of the solutions
*PLUS
Conc.: 1.7 M / Common name: ammonium sulfate

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.66 Å / Num. obs: 8624 / % possible obs: 64 % / Observed criterion σ(I): 1.5 / Num. measured all: 13413

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Processing

Software
NameClassification
X-PLORrefinement
PROLSQrefinement
RefinementResolution: 2.66→6 Å /
RfactorNum. reflection
Rwork0.191 -
obs0.191 7759
Refinement stepCycle: LAST / Resolution: 2.66→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 61 0 0 3408
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na0.033
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
X-RAY DIFFRACTIONp_bond_d0.0180.025
X-RAY DIFFRACTIONp_angle_d0.0330.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0260.03
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_restr0.0110.025
X-RAY DIFFRACTIONp_chiral_restr0.1550.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.3
X-RAY DIFFRACTIONp_multtor_nbd0.2430.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2270.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.63
X-RAY DIFFRACTIONp_staggered_tor2315
X-RAY DIFFRACTIONp_orthonormal_tor2915
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.66 Å / Lowest resolution: 6 Å / Num. reflection obs: 7759 / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.7 Å2

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