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- PDB-3rpx: Crystal structure of complement component 1, q subcomponent bindi... -

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Basic information

Entry
Database: PDB / ID: 3rpx
TitleCrystal structure of complement component 1, q subcomponent binding protein, C1QBP
ComponentsComplement component 1 Q subcomponent-binding protein
KeywordsPROTEIN BINDING / structural genomics / structural genomics consortium / mitochondrion matrix / complement system / protein-binding / SGC
Function / homology
Function and homology information


adrenergic receptor binding / Apoptotic factor-mediated response / Defective Intrinsic Pathway for Apoptosis Due to p14ARF Loss of Function / negative regulation of MDA-5 signaling pathway / kininogen binding / negative regulation of RIG-I signaling pathway / negative regulation of defense response to virus / positive regulation of dendritic cell chemotaxis / hyaluronic acid binding / complement component C1q complex binding ...adrenergic receptor binding / Apoptotic factor-mediated response / Defective Intrinsic Pathway for Apoptosis Due to p14ARF Loss of Function / negative regulation of MDA-5 signaling pathway / kininogen binding / negative regulation of RIG-I signaling pathway / negative regulation of defense response to virus / positive regulation of dendritic cell chemotaxis / hyaluronic acid binding / complement component C1q complex binding / positive regulation of trophoblast cell migration / mitochondrial ribosome binding / regulation of complement activation / positive regulation of mitochondrial translation / negative regulation of interleukin-12 production / positive regulation of neutrophil chemotaxis / enzyme inhibitor activity / RHOC GTPase cycle / negative regulation of mRNA splicing, via spliceosome / transcription factor binding / negative regulation of type II interferon production / positive regulation of cell adhesion / RHOA GTPase cycle / negative regulation of double-strand break repair via homologous recombination / positive regulation of substrate adhesion-dependent cell spreading / Intrinsic Pathway of Fibrin Clot Formation / complement activation, classical pathway / RNA splicing / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytosolic ribosome assembly / mRNA processing / transcription corepressor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mitochondrial matrix / immune response / positive regulation of apoptotic process / innate immune response / mRNA binding / apoptotic process / nucleolus / negative regulation of transcription by RNA polymerase II / cell surface / mitochondrion / extracellular region / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Mitochondrial Matrix Protein; Chain A / Mitochondrial glycoprotein / Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Roll / Alpha Beta
Similarity search - Domain/homology
Complement component 1 Q subcomponent-binding protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsTempel, W. / Tong, Y. / Crombet, L. / Shen, Y. / Guan, X. / Nedyalkova, L. / Walker, J.R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Tempel, W. / Tong, Y. / Crombet, L. / Shen, Y. / Guan, X. / Nedyalkova, L. / Walker, J.R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of complement component 1, q subcomponent binding protein, C1QBP
Authors: Tempel, W. / Tong, Y. / Crombet, L. / Shen, Y. / Guan, X. / Nedyalkova, L. / Walker, J.R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Park, H.
History
DepositionApr 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement component 1 Q subcomponent-binding protein
B: Complement component 1 Q subcomponent-binding protein
C: Complement component 1 Q subcomponent-binding protein


Theoretical massNumber of molelcules
Total (without water)66,38522
Polymers66,3853
Non-polymers019
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-40 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.680, 123.770, 137.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Complement component 1 Q subcomponent-binding protein / GC1q-R protein / Glycoprotein gC1qBP / C1qBP / Hyaluronan-binding protein 1 / Mitochondrial matrix ...GC1q-R protein / Glycoprotein gC1qBP / C1qBP / Hyaluronan-binding protein 1 / Mitochondrial matrix protein p32 / p33


Mass: 22128.186 Da / Num. of mol.: 3 / Fragment: UNP residues 96-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1QBP, GC1QBP, HABP1, SF2P32 / Plasmid: pNIC-CH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q07021
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 19 / Source method: obtained synthetically
Sequence detailsTHE ORIGINAL EXPRESSION CONSTRUCT ENCOMPASSED RESIDUES 3-282 OF UNIPROT SEQUENCE Q07021. WE SUSPECT ...THE ORIGINAL EXPRESSION CONSTRUCT ENCOMPASSED RESIDUES 3-282 OF UNIPROT SEQUENCE Q07021. WE SUSPECT THAT DUE TO INTRAMOLECULAR DNA INTERACTIONS ONLY A SHORTENED SEGMENT WAS AMPLIFIED, POSSIBLY ENCODING THE REPORTED AMINO ACID SEQUENCE

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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: 3.7 Å3/Da / Density % sol: 66.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% peg1500, 0.2 M sodium chloride, 0.1 M HEPES, 5% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→40 Å / Num. obs: 28824 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 67.228 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 18.46
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.65-2.720.9722.215727209799.9
2.72-2.790.7242.815413205299.8
2.79-2.870.5793.5150462001100
2.87-2.960.4754.214566194399.8
2.96-3.060.3975.1140671873100
3.06-3.170.2797137901838100
3.17-3.290.18810.1133071777100
3.29-3.420.1313.812751170999.9
3.42-3.570.10217.8120931620100
3.57-3.750.09419.411621157999.9
3.75-3.950.0822.5109581479100
3.95-4.190.06127.1106111436100
4.19-4.480.04734.29726132699.9
4.48-4.840.044190991239100
4.84-5.30.04239.384931163100
5.3-5.930.04537.975181034100
5.93-6.840.042406833949100
6.84-8.380.0348.45653794100
8.38-11.850.02458.74364630100
11.850.02458.1182028575.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1p32

1p32


Resolution: 2.65→19.7 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9363 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: refmac, phenix, coot and the molprobity server were also used during refinement. UNK atoms were refined as water rather than omitted in order to better approximate the properties of these unknown entities.
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 1520 5.27 %THIN SHELLS (SFTOOLS)
Rwork0.1949 ---
obs0.1965 28824 --
Displacement parametersBiso max: 164.1 Å2 / Biso mean: 82.1977 Å2 / Biso min: 27.64 Å2
Baniso -1Baniso -2Baniso -3
1-16.5632 Å20 Å20 Å2
2---9.196 Å20 Å2
3----7.3672 Å2
Refine analyzeLuzzati coordinate error obs: 0.442 Å
Refinement stepCycle: LAST / Resolution: 2.65→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 19 0 3243
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1077SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes479HARMONIC5
X-RAY DIFFRACTIONt_it3298HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion450SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3422SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3298HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4484HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion17.56
LS refinement shellResolution: 2.65→2.75 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.289 159 5.34 %
Rwork0.2535 2821 -
all0.2553 2980 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.53330.97631.51221.83982.67565.61230.016-0.26030.0880.3209-0.1768-0.1931-0.0264-0.01570.1608-0.28870.0392-0.05580.3235-0.0871-0.197246.835519.510815.4839
25.1754-0.74440.24251.30660.04750.7902-0.3171-0.16150.25460.10930.1177-0.0080.0540.13050.1994-0.26040.0291-0.02160.3408-0.1224-0.22212.51523.07847.6916
314.1372-0.66992.4290.60280.76231.9219-0.2217-1.08850.40040.044-0.12240.3082-0.3538-0.31790.3441-0.20520.0551-0.16890.3428-0.304-0.314928.330538.952934.8751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A100 - 288
2X-RAY DIFFRACTION2{ B|* }B100 - 281
3X-RAY DIFFRACTION3{ C|* }C101 - 281

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