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- PDB-8eph: Crystal structure of human coagulation factor IXa (S195A), apo-fo... -

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Basic information

Entry
Database: PDB / ID: 8eph
TitleCrystal structure of human coagulation factor IXa (S195A), apo-form, DES-GLA
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
alpha-L-fucopyranose / Coagulation factor IX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 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 1.2Nov 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

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Assembly

Deposited unit
A: Coagulation factor IXa light chain
B: Coagulation factor IXa heavy chain
C: Coagulation factor IXa light chain
D: Coagulation factor IXa heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,47210
Polymers74,9834
Non-polymers4896
Water8,359464
1
A: Coagulation factor IXa light chain
B: Coagulation factor IXa heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7365
Polymers37,4912
Non-polymers2443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-31 kcal/mol
Surface area16090 Å2
MethodPISA
2
C: Coagulation factor IXa light chain
D: Coagulation factor IXa heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7365
Polymers37,4912
Non-polymers2443
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-30 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.247, 90.247, 156.347
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody Coagulation factor IXa light chain


Mass: 11316.673 Da / Num. of mol.: 2 / 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.: 2 / Mutation: S195A
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
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 464 / 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
dg9lite_soak12.12642.06Tear-drop to square
1
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Na Citrate pH 5.0; 30% Jeffamine ED-2001 pH 7.0
PH range: 5.0 - 7.0

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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: 1.88→78.16 Å / Num. obs: 52703 / % possible obs: 99.3 % / Redundancy: 6 % / Biso Wilson estimate: 24.65 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.042 / Rrim(I) all: 0.104 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 4

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.88-1.926.20.67833180.8540.2920.7499
9.01-78.165.40.0495460.9950.0240.05595.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.77 Å78.16 Å
Translation4.77 Å78.16 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, 5VYG

5jb9

5vyg


Resolution: 1.88→78.16 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.474 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1583 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 2660 5.1 %RANDOM
Rwork0.1842 ---
obs0.1855 49995 98.86 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 120.46 Å2 / Biso mean: 30.374 Å2 / Biso min: 15.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.82 Å20 Å2
3---1.64 Å2
Refinement stepCycle: final / Resolution: 1.88→78.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5058 0 24 464 5546
Biso mean--25.79 33.61 -
Num. residues----652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0185235
X-RAY DIFFRACTIONr_bond_other_d0.0010.024778
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.8557106
X-RAY DIFFRACTIONr_angle_other_deg1.0992.7411044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55923.433268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60615862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9571524
X-RAY DIFFRACTIONr_chiral_restr0.0860.2766
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021206
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: 1.88→1.928 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 193 -
Rwork0.269 3603 -
all-3796 -
obs--99.09 %

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