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

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Basic information

Entry
Database: PDB / ID: 7qot
TitleFactor XI and Plasma Kallikrein apple domain structures reveals different kininogen bound complexes
Components
  • Coagulation factor XIa heavy chain
  • Kininogen-1 light 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


coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / negative regulation of cell adhesion / plasminogen activation / negative regulation of blood coagulation / cysteine-type endopeptidase inhibitor activity / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / negative regulation of cell adhesion / plasminogen activation / negative regulation of blood coagulation / cysteine-type endopeptidase inhibitor activity / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / platelet alpha granule lumen / Peptide ligand-binding receptors / Post-translational protein phosphorylation / hormone activity / vasodilation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / heparin binding / : / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / blood microparticle / G alpha (q) signalling events / positive regulation of apoptotic process / endoplasmic reticulum lumen / inflammatory response / signaling receptor binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / membrane / 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
Kininogen-1 / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.24 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 28, 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
Revision 1.2Nov 13, 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: Coagulation factor XIa heavy chain
B: Coagulation factor XIa heavy chain
C: Kininogen-1 light chain
D: Kininogen-1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,08313
Polymers86,8434
Non-polymers1,2409
Water00
1
A: Coagulation factor XIa heavy chain
C: Kininogen-1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1527
Polymers43,4212
Non-polymers7315
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-52 kcal/mol
Surface area18220 Å2
MethodPISA
2
B: Coagulation factor XIa heavy chain
D: Kininogen-1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9316
Polymers43,4212
Non-polymers5094
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-52 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.319, 87.319, 629.548
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 333 or resid 335 through 401 or resid 403 through 404))
21(chain B and (resid 2 through 333 or resid 335 through 401 or resid 403 through 404))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSSERSER(chain A and (resid 2 through 333 or resid 335 through 401 or resid 403 through 404))AA2 - 3332 - 333
12ASNASNNAGNAG(chain A and (resid 2 through 333 or resid 335 through 401 or resid 403 through 404))AA - E335 - 401335
13SO4SO4SO4SO4(chain A and (resid 2 through 333 or resid 335 through 401 or resid 403 through 404))AG - H403 - 404
21CYSCYSSERSER(chain B and (resid 2 through 333 or resid 335 through 401 or resid 403 through 404))BB2 - 3332 - 333
22ASNASNNAGNAG(chain B and (resid 2 through 333 or resid 335 through 401 or resid 403 through 404))BB - J335 - 401335
23SO4SO4SO4SO4(chain B and (resid 2 through 333 or resid 335 through 401 or resid 403 through 404))BL - M403 - 404

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Components

#1: Protein Coagulation factor XIa heavy chain


Mass: 39972.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P03951
#2: Protein/peptide Kininogen-1 light chain


Mass: 3448.635 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
#3: 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.: 3 / 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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
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: 3.99 Å3/Da / Density % sol: 69.17 %
Crystal growTemperature: 288 K / Method: evaporation / Details: 0.1M Tris pH8, 1.5M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.796 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.796 Å / Relative weight: 1
ReflectionResolution: 3.24→75.6 Å / Num. obs: 19451 / % possible obs: 94.9 % / Redundancy: 10.8 % / Biso Wilson estimate: 55.7 Å2 / CC1/2: 0.994 / Net I/σ(I): 16.5
Reflection shellResolution: 3.241→3.369 Å / Num. unique obs: 972 / CC1/2: 0.993

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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: 2F83, 4BDX

2f83
PDB Unreleased entry

4bdx


Resolution: 3.24→73.53 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2836 1942 9.99 %
Rwork0.2508 17489 -
obs0.254 19431 80.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 261.89 Å2 / Biso mean: 60.446 Å2 / Biso min: 8.43 Å2
Refinement stepCycle: final / Resolution: 3.24→73.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5836 0 72 0 5908
Biso mean--97.22 --
Num. residues----744
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2156X-RAY DIFFRACTION13.289TORSIONAL
12B2156X-RAY DIFFRACTION13.289TORSIONAL
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 (%)
3.24-3.320.3151620.310156162338
3.32-3.410.3506680.299660267040
3.41-3.510.3613780.297970077846
3.51-3.630.3528890.279580389253
3.63-3.750.33851040.2765933103763
3.76-3.910.29361330.27011199133280
3.91-4.080.31061700.27261529169999
4.08-4.30.28771690.235415181687100
4.3-4.570.23371720.214615481720100
4.57-4.920.24211710.213615441715100
4.92-5.420.26731750.232615741749100
5.42-6.20.28431740.246115691743100
6.2-7.810.29851810.26116231804100
7.81-73.530.27211960.2641786198299

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