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- PDB-1adq: CRYSTAL STRUCTURE OF A HUMAN IGM RHEUMATOID FACTOR FAB IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1adq
TitleCRYSTAL STRUCTURE OF A HUMAN IGM RHEUMATOID FACTOR FAB IN COMPLEX WITH ITS AUTOANTIGEN IGG FC
Components
  • IGG4 REA FC
  • IGM-LAMBDA RF-AN FAB (HEAVY CHAIN)
  • IGM-LAMBDA RF-AN FAB (LIGHT CHAIN)
KeywordsCOMPLEX (IMMUNOGLOBULIN/AUTOANTIGEN) / COMPLEX (IMMUNOGLOBULIN-AUTOANTIGEN) / RHEUMATOID FACTOR AUTO-ANTIBODY COMPLEX / COMPLEX (IMMUNOGLOBULIN-AUTOANTIGEN) complex
Function / homology
Function and homology information


IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis ...IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / 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 ...: / 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 constant gamma 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsCorper, A.L. / Taussig, M.J. / Sutton, B.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of human IgM rheumatoid factor Fab bound to its autoantigen IgG Fc reveals a novel topology of antibody-antigen interaction.
Authors: Corper, A.L. / Sohi, M.K. / Bonagura, V.R. / Steinitz, M. / Jefferis, R. / Feinstein, A. / Beale, D. / Taussig, M.J. / Sutton, B.J.
#1: Journal: Immunology / Year: 1996
Title: Crystallization of a Complex between the Fab Fragment of a Human Immunoglobulin M (Igm) Rheumatoid Factor (Rf-an) and the Fc Fragment of Human Igg4
Authors: Sohi, M.K. / Corper, A.L. / Wan, T. / Steinitz, M. / Jefferis, R. / Beale, D. / He, M. / Feinstein, A. / Sutton, B.J. / Taussig, M.J.
History
DepositionFeb 18, 1997Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IGG4 REA FC
L: IGM-LAMBDA RF-AN FAB (LIGHT CHAIN)
H: IGM-LAMBDA RF-AN FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)70,7183
Polymers70,7183
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)160.350, 81.950, 64.240
Angle α, β, γ (deg.)90.00, 98.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein IGG4 REA FC


Mass: 23484.457 Da / Num. of mol.: 1 / Fragment: FC / Source method: isolated from a natural source
Details: ISOLATED FROM THE SERA OF PATIENTS WITH MULTIPLE MYELOMA
Source: (natural) Homo sapiens (human) / Cell: B-LYMPHOCYTE / Cellular location: EXTRACELLULAR / References: UniProt: P01861
#2: Antibody IGM-LAMBDA RF-AN FAB (LIGHT CHAIN)


Mass: 22567.885 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source
Details: RF-AN CELL LINE WAS PREPARED FROM PERIPHERAL BLOOD LYMPHOCYTES OF AN RA PATIENT BY TRANSFORMATION WITH EPSTEIN-BARR VIRUS
Source: (natural) Homo sapiens (human) / Cell: B-LYMPHOCYTE / Cell line: RF-AN / Cellular location: EXTRACELLULAR
#3: Antibody IGM-LAMBDA RF-AN FAB (HEAVY CHAIN)


Mass: 24665.742 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source
Details: RF-AN CELL LINE WAS PREPARED FROM PERIPHERAL BLOOD LYMPHOCYTES OF AN RA PATIENT BY TRANSFORMATION WITH EPSTEIN-BARR VIRUS
Source: (natural) Homo sapiens (human) / Cell: B-LYMPHOCYTE / Cell line: RF-AN / Cellular location: EXTRACELLULAR
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 58 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION. THE HANGING DROPS CONSISTED OF 2UL OF PROTEIN SOLUTION CONTAINING EACH PROTEIN AT 1MG/ML IN 0.1 % SODIUM AZIDE, 20MM TRIS-HCL AT PH 7.0, ...Details: CRYSTALS WERE GROWN BY HANGING DROP VAPOR DIFFUSION. THE HANGING DROPS CONSISTED OF 2UL OF PROTEIN SOLUTION CONTAINING EACH PROTEIN AT 1MG/ML IN 0.1 % SODIUM AZIDE, 20MM TRIS-HCL AT PH 7.0, MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION TO BE SCREENED. CRYSTALS WERE OBTAINED WITH RESERVOIR SOLUTIONS CONTAINING 17.5 - 22.5 % (W/V) POLYETHYLENE GLYCOL (MEAN MW 8000) IN 0.1 % SODIUM AZIDE, 100MM TRIS-HCL, PH 7.0, AT TEMPERATURES BETWEEN 17.5 AND 21.5 (CELSIUS)., vapor diffusion - hanging drop
PH range: APPROX. / Temp details: 290.5 - 294.5
Crystal grow
*PLUS
Temperature: 17.5-21.5 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mg/mlprotein1drop
20.1 %1dropNaN3
320 mMTris-HCl1drop
417.5-22.5 %(w/v)PEG80001reservoir
50.1 %1reservoirNaN3
6100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.15→15 Å / Num. obs: 14109 / % possible obs: 98.3 % / Observed criterion σ(I): 3 / Redundancy: 3.1 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 5.3
Reflection shellResolution: 3.15→3.31 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.8 / % possible all: 98.8
Reflection shell
*PLUS
% possible obs: 98.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
CCP4data reduction
AMoREphasing
X-PLOR3.1refinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FC1, 2IG2

1fc1

2ig2


Resolution: 3.15→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100000 / Data cutoff low absF: 80 / Isotropic thermal model: GROUPED B-FACTOR REFINEMENT / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED REGION A263-A300 WAS MODELED STEREOCHEMICALLY. FAB IN COMPLEX WITH ITS AUTOANTIGEN IGG FC. CONSTANT DOMAINS OF RF-AN SHOWED SIGNIFICANT DISORDER AND WERE PARTLY MODELED ...Details: DISORDERED REGION A263-A300 WAS MODELED STEREOCHEMICALLY. FAB IN COMPLEX WITH ITS AUTOANTIGEN IGG FC. CONSTANT DOMAINS OF RF-AN SHOWED SIGNIFICANT DISORDER AND WERE PARTLY MODELED STEREOCHEMICALLY. RESIDUES L51 AND L171 OCCUR IN WELL DEFINED REGIONS OF THE STRUCTURE (OCCUPANCY = 1). BOTH OCCUR IN LOOP REGIONS AND CONTINUE TO HAVE DISALLOWED PHI/PSI VALUES EVEN AFTER REBUILDING.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 756 5.6 %RANDOM
Rwork0.225 ---
obs0.225 11603 86 %-
Displacement parametersBiso mean: 33.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 3.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4977 0 0 0 4977
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
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_deg1.18
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.47
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.06
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
LS refinement shellResolution: 3.15→3.26 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.367 53 3.9 %
Rwork0.288 902 -
obs--70.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.47
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.06

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