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- PDB-9i24: Coagulation factor Xa complex with a2-loop peptide -

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Basic information

Entry
Database: PDB / ID: 9i24
TitleCoagulation factor Xa complex with a2-loop peptide
Components
  • Activated factor Xa heavy chain
  • Coagulation factor V heavy chain
  • Factor X light chain
  • GLU-GLY-ARG-chloromethyl ketone inhibitor (EGRCK)
KeywordsBLOOD CLOTTING / protease / enzyme / complex
Function / homology
Function and homology information


response to vitamin K / coagulation factor Xa / platelet alpha granule / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / COPII-mediated vesicle transport / Extrinsic Pathway of Fibrin Clot Formation ...response to vitamin K / coagulation factor Xa / platelet alpha granule / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / COPII-mediated vesicle transport / Extrinsic Pathway of Fibrin Clot Formation / blood circulation / positive regulation of TOR signaling / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation / phospholipid binding / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / extracellular vesicle / positive regulation of cell migration / endoplasmic reticulum lumen / copper ion binding / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Coagulation factor 5/8-like / : / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : ...Coagulation factor 5/8-like / : / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / F5/8 type C domain / Coagulation factor-like, Gla domain superfamily / Coagulation factor 5/8 C-terminal domain / Coagulation Factor Xa inhibitory site / Multicopper oxidase, N-terminal / Multicopper oxidase / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / Cupredoxin / EGF-like domain / Galactose-binding-like domain superfamily / 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
Similarity search - Domain/homology
Chem-0GJ / GLUTAMIC ACID / ISOLEUCINE / IMIDAZOLE / PHENYLALANINE / O-PHOSPHOTYROSINE / Coagulation factor X / Coagulation factor V
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsHuntington, J.A. / Ustok, F.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationPG/24/11721 United Kingdom
CitationJournal: Blood / Year: 2025
Title: A 3.3-Å cryo-EM structure of an engineered high-affinity human prothrombinase complex.
Authors: Fatma Işık Üstok / Alexandre Faille / James A Huntington /
Abstract: Thrombin is generated from prothrombin through cleavage at two sites by the enzyme prothrombinase, composed of factor (f) Xa and fVa. The affinity of fXa for fVa is low, with assembly and function ...Thrombin is generated from prothrombin through cleavage at two sites by the enzyme prothrombinase, composed of factor (f) Xa and fVa. The affinity of fXa for fVa is low, with assembly and function dependent on phospholipid (PL) membranes. Some snakes have evolved venom versions of fXa that bind to fVa with high affinity and efficiently activate prothrombin in the absence of PL. We created a similar high-affinity, PL-independent human prothrombinase with 17 mutations to human fXa (M17). The increase in affinity enabled cryogenic electron microscopy (cryo-EM) structure determination of M17-prothrombinase to a resolution of 3.3 Å. All protein domains were well resolved in the map, except for the Gla domain of fXa. The main contacts involve the serine protease and EGF2 domains of fXa and the A2 and A3 domains of fVa, resulting in the burying of a total surface area of 4,900 Å2. The map is of sufficient quality to resolve side chain interactions, including several key M17 mutations. To aid in the placement of the loop C-terminal to the A2 domain (a2-loop), we solved a high-resolution crystal structure of fXa in complex with a synthetic a2-peptide. The acidic a2-loop interacts with the basic heparin binding site of fXa, involving a conserved antiparallel b-strand interaction. The M17-prothrombinase structure is compatible with data from biochemical and mutagenesis research, and provides important new insights into the assembly and function of the prothrombinase complex.
History
DepositionJan 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Activated factor Xa heavy chain
L: Factor X light chain
C: Coagulation factor V heavy chain
I: GLU-GLY-ARG-chloromethyl ketone inhibitor (EGRCK)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,21714
Polymers36,8024
Non-polymers1,41510
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-49 kcal/mol
Surface area13010 Å2
Unit cell
Length a, b, c (Å)48.473, 72.419, 82.335
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules HL

#1: Protein Activated factor Xa heavy chain


Mass: 28538.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F10 / Production host: Escherichia coli (E. coli) / References: UniProt: P00742
#2: Protein Factor X light chain


Mass: 6034.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F10 / Production host: Escherichia coli (E. coli) / References: UniProt: P00742

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Protein/peptide , 2 types, 2 molecules CI

#3: Protein/peptide Coagulation factor V heavy chain


Mass: 1866.800 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The Y is phosphorylated (PTR); the N-terminus is acetylated; the C-terminus is amidated.
Source: (synth.) synthetic construct (others) / References: UniProt: P12259
#4: Protein/peptide GLU-GLY-ARG-chloromethyl ketone inhibitor (EGRCK)


Mass: 361.375 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The R is modified and the identifier OGJ is used. It is covalently linked to the catalytic Ser195 and His57.
Source: (synth.) synthetic construct (others)

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Non-polymers , 10 types, 305 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#9: Chemical ChemComp-0GJ / L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide


Type: peptide-like / Mass: 395.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28ClN6O5
#10: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-PTR / O-PHOSPHOTYROSINE / PHOSPHONOTYROSINE


Type: L-peptide linking / Mass: 261.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12NO6P / Feature type: SUBJECT OF INVESTIGATION
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 1.96 Å3/Da / Density % sol: 37.35 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: imidazole, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.70979 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.70979 Å / Relative weight: 1
ReflectionResolution: 1.2→54.38 Å / Num. obs: 89301 / % possible obs: 98.1 % / Redundancy: 13.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.3
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4305 / CC1/2: 0.672 / Rpim(I) all: 0.633 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→54.378 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.47 / SU ML: 0.028 / Cross valid method: FREE R-VALUE / ESU R: 0.037 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1718 4536 5.083 %
Rwork0.1413 84704 -
all0.143 --
obs-89240 97.832 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.469 Å2
Baniso -1Baniso -2Baniso -3
1--0.834 Å20 Å20 Å2
2--0.851 Å20 Å2
3----0.017 Å2
Refinement stepCycle: LAST / Resolution: 1.2→54.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2209 0 73 295 2577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122519
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162257
X-RAY DIFFRACTIONr_angle_refined_deg1.9771.8273430
X-RAY DIFFRACTIONr_angle_other_deg0.7311.7615198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6525333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.079520
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.72852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67610382
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.88610115
X-RAY DIFFRACTIONr_chiral_restr0.1080.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023125
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02617
X-RAY DIFFRACTIONr_nbd_refined0.3190.2522
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2280.22095
X-RAY DIFFRACTIONr_nbtor_refined0.180.21196
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21253
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2880.2215
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1490.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1210.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2840.213
X-RAY DIFFRACTIONr_nbd_other0.2110.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.218
X-RAY DIFFRACTIONr_mcbond_it5.8161.8041284
X-RAY DIFFRACTIONr_mcbond_other5.8151.8041283
X-RAY DIFFRACTIONr_mcangle_it8.1273.2391627
X-RAY DIFFRACTIONr_mcangle_other8.1253.2391628
X-RAY DIFFRACTIONr_scbond_it7.5642.0761235
X-RAY DIFFRACTIONr_scbond_other7.5612.0771236
X-RAY DIFFRACTIONr_scangle_it10.6013.6941801
X-RAY DIFFRACTIONr_scangle_other10.5983.6951802
X-RAY DIFFRACTIONr_lrange_it15.30621.8962905
X-RAY DIFFRACTIONr_lrange_other15.30421.8982906
X-RAY DIFFRACTIONr_rigid_bond_restr4.0634776
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.2-1.2310.2683170.25661070.25766710.9560.95896.29740.246
1.231-1.2650.2583370.23759300.23864900.9640.96796.56390.225
1.265-1.3020.2313170.21758200.21863390.9680.97496.81340.202
1.302-1.3420.2163060.1956580.19261580.9680.97996.84960.172
1.342-1.3860.1892820.16455230.16559580.9790.98497.4320.144
1.386-1.4340.192930.15352930.15557390.9780.98697.3340.132
1.434-1.4880.172870.13251450.13455680.9840.98997.55750.113
1.488-1.5490.1522650.11950130.12153980.9850.99197.7770.103
1.549-1.6180.1472490.10848300.1151850.9860.99397.95560.094
1.618-1.6970.1432650.10145430.10348990.9880.99498.14250.089
1.697-1.7880.1432330.09844220.10147330.9870.99498.3520.089
1.788-1.8970.1541950.1141820.11244500.9870.99498.35960.101
1.897-2.0270.152090.12239630.12442280.9880.99398.67550.114
2.027-2.190.1681790.12536880.12739140.9850.99298.79920.118
2.19-2.3980.1512000.11733950.11936250.9880.99299.17240.11
2.398-2.6810.1481680.12130970.12332960.9870.99199.05950.115
2.681-3.0940.1611490.13927600.14129240.9850.98899.4870.133
3.094-3.7860.1871200.13523750.13825070.9790.98899.52130.128
3.786-5.3420.156940.15218640.15319640.9880.98899.69450.145
5.342-54.3780.259710.25910960.25911720.9760.96799.57340.245

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