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- PDB-8epc: Crystal structure of human coagulation factor IXa (S195A), apo-form -

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Basic information

Entry
Database: PDB / ID: 8epc
TitleCrystal structure of human coagulation factor IXa (S195A), apo-form
Components
  • Coagulation factor IXa heavy chain
  • Coagulation factor IXa light chain
KeywordsBLOOD CLOTTING / coagulation factor IX / apo- form / hydrolase
Function / homology
Function and homology information


Defective F9 secretion / coagulation factor IXa / Defective gamma-carboxylation of F9 / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Protein hydroxylation ...Defective F9 secretion / coagulation factor IXa / Defective gamma-carboxylation of F9 / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Protein hydroxylation / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Golgi lumen / blood coagulation / : / endopeptidase activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / 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 ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / 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. / EGF-like domain / 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
Coagulation factor IX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsKolyadko, V.N. / Krishnaswamy, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01HL139420 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: An RNA aptamer exploits exosite-dependent allostery to achieve specific inhibition of coagulation factor IXa.
Authors: Kolyadko, V.N. / Layzer, J.M. / Perry, K. / Sullenger, B.A. / Krishnaswamy, S.
History
DepositionOct 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 30, 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 IXa light chain
B: Coagulation factor IXa heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4823
Polymers33,4422
Non-polymers401
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-21 kcal/mol
Surface area13310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.975, 67.975, 109.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Coagulation factor IXa light chain


Mass: 7267.338 Da / Num. of mol.: 1 / Fragment: furin cleavage site (RRKR) inserted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F9 / Plasmid: phCMV1-WPRE / Details (production host): propeptide of mouse IgG HC / Cell (production host): fibroblast / Cell line (production host): AV12 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P00740
#2: Protein Coagulation factor IXa heavy chain


Mass: 26174.818 Da / Num. of mol.: 1 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F9 / Plasmid: phCMV1-WPRE / Cell (production host): fibroblast / Cell line (production host): AV12 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P00740
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
de9soakapt_a5_12.19343.84trigonal bar
1
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 40% Glycerol Ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.51→58.87 Å / Num. obs: 10405 / % possible obs: 99.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 72.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.026 / Rrim(I) all: 0.054 / Net I/σ(I): 17.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.51-2.614.20.861477311400.6180.470.9881.698
9.05-58.873.60.0269672680.9990.0150.0344.797.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.28 Å58.87 Å
Translation5.28 Å58.87 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JB9

5jb9


Resolution: 2.51→58.87 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 27.787 / SU ML: 0.272 / SU R Cruickshank DPI: 0.732 / Cross valid method: THROUGHOUT / ESU R: 0.732 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2807 512 4.9 %RANDOM
Rwork0.2313 ---
obs0.2337 9865 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 174.61 Å2 / Biso mean: 86.776 Å2 / Biso min: 52.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å2-0 Å2
2--0.05 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 2.51→58.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 1 4 2119
Biso mean--104.54 61.04 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0172163
X-RAY DIFFRACTIONr_bond_other_d0.0010.022020
X-RAY DIFFRACTIONr_angle_refined_deg0.9681.8492934
X-RAY DIFFRACTIONr_angle_other_deg0.8932.7294647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3085266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49322.87108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3715356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5011511
X-RAY DIFFRACTIONr_chiral_restr0.0540.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022442
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02496
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.575 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 35 -
Rwork0.306 690 -
all-725 -
obs--96.93 %
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)
15.15741.46631.12417.54384.11754.2531-0.125-0.0554-0.18810.64030.2899-0.6550.39540.6306-0.1650.11880.0992-0.06240.1897-0.01230.2583-5.65414.3922.953
24.3633-0.82440.41396.78081.63743.7567-0.11020.45850.4336-0.75230.06230.5258-0.5345-0.1340.04790.1329-0.0064-0.05440.08490.0580.1349-25.19620.173-12.179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A86 - 137
2X-RAY DIFFRACTION2B16 - 245

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