[English] 日本語
Yorodumi
- PDB-7fbp: FXIIa-cMCoFx1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fbp
TitleFXIIa-cMCoFx1 complex
Components
  • Coagulation factor XIIa light chainFactor XII
  • cMCoFx1
KeywordsBLOOD CLOTTING / Serine protease / Inhibitor / macrocyclic peptide / Cyclotide
Function / homology
Function and homology information


coagulation factor XIIa / plasma kallikrein-kinin cascade / Factor XII activation / Defective SERPING1 causes hereditary angioedema / response to misfolded protein / positive regulation of plasminogen activation / blood coagulation, intrinsic pathway / positive regulation of fibrinolysis / misfolded protein binding / zymogen activation ...coagulation factor XIIa / plasma kallikrein-kinin cascade / Factor XII activation / Defective SERPING1 causes hereditary angioedema / response to misfolded protein / positive regulation of plasminogen activation / blood coagulation, intrinsic pathway / positive regulation of fibrinolysis / misfolded protein binding / zymogen activation / Defective factor XII causes hereditary angioedema / protein autoprocessing / rough endoplasmic reticulum / positive regulation of blood coagulation / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / protein processing / blood coagulation / collagen-containing extracellular matrix / serine-type endopeptidase activity / innate immune response / calcium ion binding / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
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. ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsSengoku, T. / Liu, W. / de Veer, S.J. / Huang, Y.H. / Okada, C. / Zdenek, C.N. / Fry, B.G. / Swedberg, J.E. / Passioura, T. / Craik, D.J. ...Sengoku, T. / Liu, W. / de Veer, S.J. / Huang, Y.H. / Okada, C. / Zdenek, C.N. / Fry, B.G. / Swedberg, J.E. / Passioura, T. / Craik, D.J. / Suga, H. / Ogata, K.
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: An Ultrapotent and Selective Cyclic Peptide Inhibitor of Human beta-Factor XIIa in a Cyclotide Scaffold.
Authors: Liu, W. / de Veer, S.J. / Huang, Y.H. / Sengoku, T. / Okada, C. / Ogata, K. / Zdenek, C.N. / Fry, B.G. / Swedberg, J.E. / Passioura, T. / Craik, D.J. / Suga, H.
History
DepositionJul 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Coagulation factor XIIa light chain
B: cMCoFx1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7383
Polymers29,5832
Non-polymers1,1551
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint13 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.190, 76.830, 41.020
Angle α, β, γ (deg.)90.000, 91.392, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Coagulation factor XIIa light chain / Factor XII / Beta-factor XIIa part 2 / FXIIa


Mass: 25941.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00748
#2: Protein/peptide cMCoFx1


Mass: 3642.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1155.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-3DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-1/a4-b1_b4-c1_c3-d1_d3-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpN]{}}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200mM sodium acetate trihydrate pH 7.0, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→41.01 Å / Num. obs: 65611 / % possible obs: 99.6 % / Redundancy: 3.83 % / Biso Wilson estimate: 28.87 Å2 / CC1/2: 0.966 / Net I/σ(I): 8.89
Reflection shellResolution: 1.99→2.11 Å / Num. unique obs: 2745 / CC1/2: 0.572 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B77

6b77


Resolution: 1.99→41.01 Å / SU ML: 0.2891 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.9954
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2475 1699 9.94 %
Rwork0.1983 15398 -
obs0.2031 17097 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.81 Å2
Refinement stepCycle: LAST / Resolution: 1.99→41.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 75 148 2237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00452138
X-RAY DIFFRACTIONf_angle_d0.72892909
X-RAY DIFFRACTIONf_chiral_restr0.0464333
X-RAY DIFFRACTIONf_plane_restr0.005375
X-RAY DIFFRACTIONf_dihedral_angle_d19.4135774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.050.35671370.30151292X-RAY DIFFRACTION99.37
2.05-2.110.32531390.27511270X-RAY DIFFRACTION99.37
2.11-2.190.30321380.26661259X-RAY DIFFRACTION99.29
2.19-2.280.28881510.25931276X-RAY DIFFRACTION99.44
2.28-2.380.32211400.21761283X-RAY DIFFRACTION99.93
2.38-2.510.30211460.21971265X-RAY DIFFRACTION99.79
2.51-2.660.27291360.21561293X-RAY DIFFRACTION99.65
2.66-2.870.24041350.19961284X-RAY DIFFRACTION99.58
2.87-3.160.26311470.18851279X-RAY DIFFRACTION99.93
3.16-3.620.24491430.18211294X-RAY DIFFRACTION99.93
3.62-4.550.1911410.16131303X-RAY DIFFRACTION99.79
4.56-41.010.20951460.17621300X-RAY DIFFRACTION99.45
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.20427212871-0.1141982734970.4864626073174.1679665701-1.334841584713.24401348678-0.00262213316621-0.08266022791690.0111020362460.2923725109520.01957449039890.136152628534-0.0875835148831-0.0355524831479-0.0153821148520.1471280941180.00232818161330.01128142523010.179883473393-0.003440159507960.2453214378062.292-1.718.745
22.816923605690.5379983769640.355524342113.279936910940.382167560151.967139672150.0547796549048-0.0547043082886-0.1315263261680.121359856591-0.00738590797365-0.00534414151040.2340159265460.0341022271385-0.01665622537750.2256494175970.02067443180640.0216341821970.1862515054460.01495111292090.2406669595734.843-6.1857.791
34.205433718822.18870622824-1.263430562884.57611693810.4327153311354.47232620537-0.1394073489940.0973029475688-0.0130861199068-0.262803988325-0.039704060069-0.0871051562385-0.1210503906430.08008268077530.08165781468610.2380619100620.0134407069291-0.0734956301970.2077966297090.07720850602670.2261274629253.7738.474-2.789
42.83524767591-0.612798223640.4602932340163.09748991114-0.5096307601222.4259719286-0.007642751423860.1274203423230.132006905685-0.128515417281-0.0226821938704-0.288969190006-0.0930378412350.0556512344110.00116355332460.164214191632-0.02210269102590.03136804388260.186374040162-0.01296189808190.23046269798813.7474.253-1.309
54.728233330590.427740647451.343792046875.043202153532.695076256564.41461303751-0.004103291114370.2052287983020.3757485003390.440644992489-0.09938685279180.23741374724-0.812981043952-0.210210540199-0.01480339740350.407417783364-0.02351110516190.006520126124160.2664935424420.05070309276290.3990838889814.98515.39811.699
68.68857728096-0.8019719329981.288156514495.70913652796-2.698766400027.028636826180.253921709915-0.333472374245-0.5286234008940.673810307464-0.201115300790.562214537056-0.380050495005-0.400783930968-0.1030450312470.421467257608-0.000136083704966-0.009581275886290.28977745594-0.0254454276210.415734965913.24418.91811.772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 373:427 )A373 - 427
2X-RAY DIFFRACTION2( CHAIN A AND RESID 428:504 )A428 - 504
3X-RAY DIFFRACTION3( CHAIN A AND RESID 505:532 )A505 - 532
4X-RAY DIFFRACTION4( CHAIN A AND RESID 533:613 )A533 - 613
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:14 )B1 - 14
6X-RAY DIFFRACTION6( CHAIN B AND RESID 15:34 )B15 - 34

+
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