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- PDB-7qox: Factor XI and Plasma Kallikrein apple domain structures reveals d... -

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Basic information

Entry
Database: PDB / ID: 7qox
TitleFactor XI and Plasma Kallikrein apple domain structures reveals different kininogen bound complexes
Components
  • Kininogen-1 light chain
  • Plasma kallikrein heavy chain
KeywordsBLOOD CLOTTING / Plasma kallikrein (PK) / High molecular weight kininogen (HK) / Factor XII (FXII) / Factor XI (FXI) / Factor IX (FIX) / bradykinin (BK)
Function / homology
Function and homology information


plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / negative regulation of cell adhesion / zymogen activation / plasminogen activation / Defective factor XII causes hereditary angioedema / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase inhibitor activity ...plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / negative regulation of cell adhesion / zymogen activation / plasminogen activation / Defective factor XII causes hereditary angioedema / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase inhibitor activity / negative regulation of blood coagulation / fibrinolysis / negative regulation of proteolysis / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / platelet alpha granule lumen / Post-translational protein phosphorylation / hormone activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / vasodilation / Platelet degranulation / heparin binding / positive regulation of cytosolic calcium ion concentration / : / G alpha (i) signalling events / G alpha (q) signalling events / blood microparticle / positive regulation of apoptotic process / inflammatory response / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / plasma membrane
Similarity search - Function
HMW kininogen / Kininogen-type cystatin domain / Kininogen-type cystatin domain profile. / : / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Hepatocyte Growth Factor / Hepatocyte Growth Factor / Cystatin domain / Cystatin-like domain ...HMW kininogen / Kininogen-type cystatin domain / Kininogen-type cystatin domain profile. / : / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Hepatocyte Growth Factor / Hepatocyte Growth Factor / Cystatin domain / Cystatin-like domain / Cystatin domain / Apple domain. / Apple domain / APPLE domain / Cystatin superfamily / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / 3-Layer(bba) Sandwich / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-PG6 / Kininogen-1 / Plasma kallikrein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.32 Å
AuthorsLi, C. / Awital, B. / Wong, S. / Dreveny, I. / Meijers, J. / Emsley, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationRG/12/9/29775 United Kingdom
CitationJournal: J Thromb Haemost / Year: 2019
Title: Plasma kallikrein structure reveals apple domain disc rotated conformation compared to factor XI.
Authors: Li, C. / Voos, K.M. / Pathak, M. / Hall, G. / McCrae, K.R. / Dreveny, I. / Li, R. / Emsley, J.
History
DepositionDec 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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
A: Plasma kallikrein heavy chain
B: Plasma kallikrein heavy chain
D: Kininogen-1 light chain
C: Kininogen-1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,68622
Polymers88,7974
Non-polymers2,88918
Water5,945330
1
A: Plasma kallikrein heavy chain
C: Kininogen-1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,77310
Polymers44,3982
Non-polymers1,3758
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint5 kcal/mol
Surface area17210 Å2
MethodPISA
2
B: Plasma kallikrein heavy chain
D: Kininogen-1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,91312
Polymers44,3982
Non-polymers1,51510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint4 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.543, 68.258, 120.311
Angle α, β, γ (deg.)90.000, 96.550, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 317 or resid 319 through 323 or resid 326 through 358 or resid 401))
21(chain B and (resid 1 through 358 or resid 402))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 317 or resid 319 through 323 or resid 326 through 358 or resid 401))A1 - 317
121(chain A and (resid 1 through 317 or resid 319 through 323 or resid 326 through 358 or resid 401))A319 - 323
131(chain A and (resid 1 through 317 or resid 319 through 323 or resid 326 through 358 or resid 401))A326 - 358
141(chain A and (resid 1 through 317 or resid 319 through 323 or resid 326 through 358 or resid 401))A401
211(chain B and (resid 1 through 358 or resid 402))B0

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Components

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Protein / Protein/peptide / Sugars , 3 types, 6 molecules ABDC

#1: Protein Plasma kallikrein heavy chain


Mass: 41134.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLKB1, KLK3 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P03952
#2: Protein/peptide Kininogen-1 light chain


Mass: 3263.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KNG1, BDK, KNG / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01042
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 346 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#8: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 288 K / Method: evaporation
Details: Morpheus screen H9 condition: 0.1M amino acids, 0.1M buffer system 3 pH8.5, 30% precipitant mix 1.

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.32→29.64 Å / Num. obs: 38760 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.46 Å2 / CC1/2: 0.987 / Net I/σ(I): 7.6
Reflection shellResolution: 2.32→2.4 Å / Num. unique obs: 9002 / CC1/2: 0.597

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I58

6i58


Resolution: 2.32→29.64 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2526 1935 4.99 %
Rwork0.1993 36825 -
obs0.2019 38760 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.07 Å2 / Biso mean: 33.7441 Å2 / Biso min: 14.06 Å2
Refinement stepCycle: final / Resolution: 2.32→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5847 0 191 330 6368
Biso mean--43.76 36 -
Num. residues----745
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2144X-RAY DIFFRACTION5.492TORSIONAL
12B2144X-RAY DIFFRACTION5.492TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.32-2.380.32651380.26472449258794
2.38-2.440.29511330.249926352768100
2.44-2.510.29771480.250726302778100
2.51-2.590.31281200.250226212741100
2.59-2.680.3061170.25326532770100
2.68-2.790.33481400.239326382778100
2.79-2.920.2831520.222726132765100
2.92-3.070.28761510.206926602811100
3.07-3.260.2571410.199926512792100
3.26-3.520.24081400.18212627276799
3.52-3.870.25131510.17012607275899
3.87-4.430.20621460.15852630277699
4.43-5.570.19311200.16712684280499
5.57-29.640.21811380.205427272865100

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