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- PDB-6szw: Asymmetric complex of Factor XII and kininogen with gC1qR/C1QBP/P... -

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Basic information

Entry
Database: PDB / ID: 6szw
TitleAsymmetric complex of Factor XII and kininogen with gC1qR/C1QBP/P32 is governed by allostery
Components
  • Coagulation factor XIIFactor XII
  • Complement component 1 Q subcomponent-binding protein, mitochondrial
KeywordsBLOOD CLOTTING / Contact activation
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 / coagulation factor XIIa / plasma kallikrein-kinin cascade / negative regulation of RIG-I signaling pathway / Factor XII activation / Defective SERPING1 causes hereditary angioedema ...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 / coagulation factor XIIa / plasma kallikrein-kinin cascade / negative regulation of RIG-I signaling pathway / Factor XII activation / Defective SERPING1 causes hereditary angioedema / response to misfolded protein / negative regulation of defense response to virus / positive regulation of dendritic cell chemotaxis / hyaluronic acid binding / complement component C1q complex binding / positive regulation of plasminogen activation / positive regulation of trophoblast cell migration / mitochondrial ribosome binding / blood coagulation, intrinsic pathway / regulation of complement activation / positive regulation of mitochondrial translation / positive regulation of fibrinolysis / negative regulation of interleukin-12 production / misfolded protein binding / positive regulation of neutrophil chemotaxis / zymogen activation / RHOC GTPase cycle / Defective factor XII causes hereditary angioedema / negative regulation of mRNA splicing, via spliceosome / transcription factor binding / protein autoprocessing / negative regulation of type II interferon production / positive regulation of cell adhesion / RHOA GTPase cycle / rough endoplasmic reticulum / positive regulation of blood coagulation / complement activation, classical pathway / positive regulation of substrate adhesion-dependent cell spreading / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / cytosolic ribosome assembly / RNA splicing / phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein processing / mRNA processing / transcription corepressor activity / blood coagulation / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mitochondrial matrix / immune response / positive regulation of apoptotic process / serine-type endopeptidase activity / mRNA binding / innate immune response / apoptotic process / calcium ion binding / nucleolus / negative regulation of transcription by RNA polymerase II / cell surface / mitochondrion / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Coagulation factor XII/hepatocyte growth factor activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain ...Mitochondrial glycoprotein / Mitochondrial glycoprotein superfamily / Mitochondrial glycoprotein / Coagulation factor XII/hepatocyte growth factor activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / EGF-like domain / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Epidermal growth factor-like domain. / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Coagulation factor XII / Complement component 1 Q subcomponent-binding protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsKaira, B.G. / Emsley, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationRG/12/9/29775 United Kingdom
CitationJournal: Blood / Year: 2020
Title: Factor XII and kininogen asymmetric assembly with gC1qR/C1QBP/P32 is governed by allostery.
Authors: Kaira, B.G. / Slater, A. / McCrae, K.R. / Dreveny, I. / Sumya, U. / Mutch, N.J. / Searle, M. / Emsley, J.
History
DepositionOct 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: Complement component 1 Q subcomponent-binding protein, mitochondrial
C: Complement component 1 Q subcomponent-binding protein, mitochondrial
D: Coagulation factor XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1367
Polymers79,9404
Non-polymers1963
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Assembly is zinc dependent
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-123 kcal/mol
Surface area29940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.290, 71.560, 115.857
Angle α, β, γ (deg.)90.000, 110.640, 90.000
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 74 - 282 / Label seq-ID: 1 - 209

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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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: 23826.105 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1QBP, GC1QBP, HABP1, SF2P32 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07021
#2: Protein Coagulation factor XII / Factor XII / Hageman factor / HAF


Mass: 8461.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F12 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P00748, coagulation factor XIIa
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium cacodylate, 0.1 M calcium acetate, 12% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.69 - 2.07
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2015
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.691
22.071
ReflectionResolution: 3.14→90.99 Å / Num. obs: 14379 / % possible obs: 99.8 % / Redundancy: 3.1 % / CC1/2: 0.953 / Rmerge(I) obs: 0.109 / Net I/σ(I): 6.4
Reflection shellResolution: 3.14→3.36 Å / Num. unique obs: 2571 / CC1/2: 0.793

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P32

1p32


Resolution: 3.14→90.99 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.866 / SU B: 25.916 / SU ML: 0.432 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.472 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 725 5 %RANDOM
Rwork0.1952 ---
obs0.1981 13647 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 182.26 Å2 / Biso mean: 76.668 Å2 / Biso min: 33.92 Å2
Baniso -1Baniso -2Baniso -3
1-2.11 Å20 Å2-6.41 Å2
2---2.99 Å20 Å2
3---4.45 Å2
Refinement stepCycle: final / Resolution: 3.14→90.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4725 0 3 11 4739
Biso mean--74.78 48.1 -
Num. residues----588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194817
X-RAY DIFFRACTIONr_bond_other_d0.0060.024442
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9466513
X-RAY DIFFRACTIONr_angle_other_deg0.95310271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0435578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32525.691246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.55215850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7031515
X-RAY DIFFRACTIONr_chiral_restr0.0790.2727
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025415
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021072
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A103180.12
12B103180.12
21A100040.13
22C100040.13
31B100580.13
32C100580.13
LS refinement shellResolution: 3.14→3.221 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 50 -
Rwork0.305 988 -
all-1038 -
obs--99.71 %

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