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- PDB-7te3: Crystal Structure of a Double Loop Deletion Mutant in gC1qR/C1qBP... -

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Basic information

Entry
Database: PDB / ID: 7te3
TitleCrystal Structure of a Double Loop Deletion Mutant in gC1qR/C1qBP/HABP-1
ComponentsComplement component 1 Q subcomponent-binding protein, mitochondrial
KeywordsIMMUNE SYSTEM / complement / C1q-binding protein / coagulation
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 / 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 / complement activation, classical pathway / positive regulation of substrate adhesion-dependent cell spreading / Intrinsic Pathway of Fibrin Clot Formation / cytosolic ribosome assembly / RNA splicing / phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / mRNA binding / innate immune response / 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 glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein
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: 2.2 Å
AuthorsGeisbrecht, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140852 United States
CitationJournal: Front Immunol / Year: 2022
Title: gC1qR/C1qBP/HABP-1: Structural Analysis of the Trimeric Core Region, Interactions With a Novel Panel of Monoclonal Antibodies, and Their Influence on Binding to FXII.
Authors: Zhang, Y. / Vontz, A.J. / Kallenberger, E.M. / Xu, X. / Ploscariu, N.T. / Ramyar, K.X. / Garcia, B.L. / Ghebrehiwet, B. / Geisbrecht, B.V.
History
DepositionJan 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Complement component 1 Q subcomponent-binding protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)20,0301
Polymers20,0301
Non-polymers00
Water72140
1
A: Complement component 1 Q subcomponent-binding protein, mitochondrial

A: Complement component 1 Q subcomponent-binding protein, mitochondrial

A: Complement component 1 Q subcomponent-binding protein, mitochondrial


Theoretical massNumber of molelcules
Total (without water)60,0913
Polymers60,0913
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6060 Å2
ΔGint-37 kcal/mol
Surface area25250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.529, 80.529, 114.552
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Complement component 1 Q subcomponent-binding protein, mitochondrial / ASF/SF2-associated protein p32 / Glycoprotein gC1qBP / C1qBP / Hyaluronan-binding protein 1 / ...ASF/SF2-associated protein p32 / Glycoprotein gC1qBP / C1qBP / Hyaluronan-binding protein 1 / Mitochondrial matrix protein p32 / gC1q-R protein / p33 / SF2AP32


Mass: 20030.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1QBP, GC1QBP, HABP1, SF2P32 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q07021
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M BisTris-HCl pH 6.5, 0.1 M sodium chloride, 1.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 11799 / % possible obs: 99.9 % / Redundancy: 20.3 % / Biso Wilson estimate: 45.4 Å2 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.032 / Rrim(I) all: 0.147 / Χ2: 1.008 / Net I/σ(I): 6 / Num. measured all: 239844
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.2813.81.86511220.5440.4991.9361.03799.6
2.28-2.3718.91.70511590.750.3961.7511.009100
2.37-2.4821.71.37111390.8690.2971.4041.031100
2.48-2.6121.80.92811690.9350.2010.951.033100
2.61-2.7721.80.59911500.9690.1290.6131.018100
2.77-2.9921.70.36311680.9890.0790.3710.982100
2.99-3.2921.60.19211700.9960.0420.1970.985100
3.29-3.7621.50.11711830.9980.0260.121.019100
3.76-4.7421.10.07912150.9990.0180.0811.016100
4.74-5019.40.04132410.0090.0410.96399.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXv1.19.2refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P32

1p32


Resolution: 2.2→37.99 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2878 1177 10 %
Rwork0.2329 10591 -
obs0.2384 11768 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.12 Å2 / Biso mean: 55.1115 Å2 / Biso min: 29.86 Å2
Refinement stepCycle: final / Resolution: 2.2→37.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1327 0 0 40 1367
Biso mean---52.57 -
Num. residues----165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071349
X-RAY DIFFRACTIONf_angle_d0.8821822
X-RAY DIFFRACTIONf_dihedral_angle_d14.997489
X-RAY DIFFRACTIONf_chiral_restr0.051206
X-RAY DIFFRACTIONf_plane_restr0.004235
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.30.34341410.31311272141399
2.3-2.420.32671410.286212811422100
2.42-2.570.30991450.273712941439100
2.57-2.770.36781450.26613041449100
2.77-3.040.35921450.25813121457100
3.04-3.480.26851470.236713231470100
3.48-4.390.28231500.212113521502100
4.39-37.990.24921630.209514531616100

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