[English] 日本語
Yorodumi
- PDB-7qot: Factor XI and Plasma Kallikrein apple domain structures reveals d... -

+
Open data


ID or keywords:

Loading...

-
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 chainFactor XI
  • 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 / negative regulation of blood coagulation / cysteine-type endopeptidase inhibitor activity / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / negative regulation of cell adhesion / negative regulation of blood coagulation / cysteine-type endopeptidase inhibitor activity / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / platelet alpha granule lumen / negative regulation of proteolysis / 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 / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / inflammatory response / positive regulation of apoptotic process / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / zinc ion binding / extracellular region / membrane / identical protein 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. / Cystatin domain / Cystatin-like domain / Cystatin domain / Apple domain. / Apple domain ...HMW kininogen / Kininogen-type cystatin domain / Kininogen-type cystatin domain profile. / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Apple domain. / Apple domain / APPLE domain / Cystatin superfamily / PAN/Apple domain profile. / PAN domain / PAN/Apple 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
Components

#1: Protein Coagulation factor XIa heavy chain / Factor XI


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 / N-Acetylglucosamine


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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more