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- PDB-9tjx: Structure of factor VII Gla domain bound to EPCR -

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Basic information

Entry
Database: PDB / ID: 9tjx
TitleStructure of factor VII Gla domain bound to EPCR
Components
  • Endothelial protein C receptor
  • Factor VII light chain
KeywordsBLOOD CLOTTING / Factor VII / activated factor VII / EPCR / GLA DOMAIN / COMPLEX / CALCIUM IONS
Function / homology
Function and homology information


negative regulation of coagulation / coagulation factor VIIa / response to Thyroid stimulating hormone / response to astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to carbon dioxide / serine-type peptidase complex / response to genistein / response to vitamin K ...negative regulation of coagulation / coagulation factor VIIa / response to Thyroid stimulating hormone / response to astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to carbon dioxide / serine-type peptidase complex / response to genistein / response to vitamin K / positive regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of leukocyte chemotaxis / response to thyroxine / response to cholesterol / positive regulation of positive chemotaxis / response to growth hormone / : / positive regulation of blood coagulation / animal organ regeneration / positive regulation of TOR signaling / 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 / BMAL1:CLOCK,NPAS2 activates circadian expression / serine-type peptidase activity / Cell surface interactions at the vascular wall / circadian rhythm / protein processing / response to estrogen / Golgi lumen / blood coagulation / response to estradiol / extracellular matrix / signaling receptor activity / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / focal adhesion / calcium ion binding / centrosome / perinuclear region of cytoplasm / cell surface / : / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Endothelial protein C receptor / MHC-I family 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. ...Endothelial protein C receptor / MHC-I family 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 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / 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
PHOSPHATIDYLETHANOLAMINE / Coagulation factor VII / Endothelial protein C receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLopez-Sagaseta, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2022-139888NB-I00 Spain
CitationJournal: Blood Adv / Year: 2026
Title: Structure of Factor VII Gla domain bound to EPCR.
Authors: Lopez-Sagaseta, J. / Dichiara-Rodriguez, M.G.
History
DepositionDec 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endothelial protein C receptor
B: Endothelial protein C receptor
C: Endothelial protein C receptor
D: Endothelial protein C receptor
L: Factor VII light chain
E: Factor VII light chain
F: Factor VII light chain
R: Factor VII light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,04949
Polymers105,6208
Non-polymers6,42941
Water543
1
A: Endothelial protein C receptor
E: Factor VII light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,31313
Polymers26,4052
Non-polymers1,90811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endothelial protein C receptor
L: Factor VII light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,00513
Polymers26,4052
Non-polymers1,60011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endothelial protein C receptor
R: Factor VII light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,70112
Polymers26,4052
Non-polymers1,29610
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endothelial protein C receptor
F: Factor VII light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,03011
Polymers26,4052
Non-polymers1,6259
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)278.406, 44.222, 111.252
Angle α, β, γ (deg.)90.000, 93.009, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 10 and (name N or name...
d_2ens_1(chain "B" and ((resid 10 and (name N or name...
d_3ens_1(chain "C" and ((resid 10 and (name N or name...
d_4ens_1(chain "D" and (resid 10 through 29 or (resid 30...
d_1ens_2(chain "E" and (resid 1 through 8 or (resid 9...
d_2ens_2(chain "F" and (resid 1 through 8 or (resid 9...
d_3ens_2(chain "L" and (resid 1 through 8 or (resid 9...
d_4ens_2(chain "R" and (resid 1 through 31 or (resid 32...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ARGARGLEULEUAA10 - 10312 - 105
d_12ens_1ALAALAILEILEAA110 - 177112 - 179
d_21ens_1ARGARGLEULEUBB10 - 10312 - 105
d_22ens_1ALAALAILEILEBB110 - 177112 - 179
d_31ens_1ARGARGILEILECC10 - 17712 - 179
d_41ens_1ARGARGILEILEDD10 - 17712 - 179
d_11ens_2ALAALALYSLYSEF1 - 321 - 32
d_21ens_2ALAALALYSLYSFG1 - 321 - 32
d_31ens_2ALAALALYSLYSLE1 - 321 - 32
d_41ens_2ALAALALYSLYSRH1 - 321 - 32

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.99938714374216, 0.00088464115705711, -0.034993632748251), (0.00094801000984382, -0.99999794084911, 0.0017943172971216), (-0.034991973364151, -0.0018263919526636, -0.9993859245019)-0.29184106667249, 35.658226897769, 107.88201952396
2given(-0.15291888763495, -0.96168230726884, -0.22755868186157), (-0.95607895067195, 0.085701648471377, 0.28030031668071), (-0.25005770111418, 0.26042727840104, -0.9325496119661)-25.204972093585, -31.838410450551, 39.316505798529
3given(-0.11400309102526, -0.9768524495557, -0.18100438401795), (0.96361163141698, -0.064386020738039, -0.25943605017697), (0.24177658909537, -0.20399444142073, 0.94864658795299)-26.117465238007, 66.99003152737, 68.488557849837
4given(-0.19780996705126, -0.95885100810786, -0.20365647837897), (0.95490678081012, -0.14156423856147, -0.26098391966436), (0.22141422018028, -0.24609817270971, 0.94361614679429)-27.155869691872, 68.984681084926, 69.709138155458
5given(0.99801128947277, -0.022867492084225, -0.058741330344885), (-0.022963614279608, -0.99973583883026, -0.00096175754019216), (-0.058703820183412, 0.0023087581351583, -0.99827277391089)1.2358006318284, 35.488197932708, 107.22445183832
6given(-0.21589485186898, -0.93720672484832, -0.27392146289687), (-0.94550588303154, 0.13063591585136, 0.29824969847833), (-0.243737641921, 0.32338492913054, -0.91433809366231)-25.354633927503, -33.461243392409, 36.994792720584

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDLEFR

#1: Protein
Endothelial protein C receptor / Activated protein C receptor / APC receptor / Endothelial cell protein C receptor


Mass: 22214.756 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Purification tag was removed prior to crystallization. A non-native GP motif (3C site) is expected to be still present in the protein used for crystallization.
Source: (gene. exp.) Homo sapiens (human) / Gene: PROCR, EPCR / Production host: Cricetus cricetus (black-bellied hamster) / References: UniProt: Q9UNN8
#2: Protein/peptide
Factor VII light chain


Mass: 4190.295 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08709

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Sugars , 4 types, 4 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#8: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
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

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Non-polymers , 6 types, 40 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ca
#10: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

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

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M Tris PH 8.5, 12 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XAIRA / Wavelength: 0.97923 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 21, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 3→43.67 Å / Num. obs: 25876 / % possible obs: 93 % / Redundancy: 3 % / Biso Wilson estimate: 48.83 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.106 / Rrim(I) all: 0.187 / Net I/σ(I): 4.2
Reflection shellResolution: 3→3.18 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4440 / CC1/2: 0.705 / Rpim(I) all: 0.326 / Rrim(I) all: 0.583

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→43.67 Å / SU ML: 0.4512 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 31.2981
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2954 1249 4.81 %
Rwork0.2416 44726 -
obs0.2442 25876 88.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.88 Å2
Refinement stepCycle: LAST / Resolution: 3→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6407 0 349 3 6759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216892
X-RAY DIFFRACTIONf_angle_d0.61269385
X-RAY DIFFRACTIONf_chiral_restr0.04031022
X-RAY DIFFRACTIONf_plane_restr0.00411192
X-RAY DIFFRACTIONf_dihedral_angle_d14.93432605
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.50558929862071
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.6120975396639
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.63952634430137
ens_2d_2FEX-RAY DIFFRACTIONTorsion NCS0.43042791370641
ens_2d_3FEX-RAY DIFFRACTIONTorsion NCS0.31259619937804
ens_2d_4FEX-RAY DIFFRACTIONTorsion NCS0.51113012316104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.33631520.28793060X-RAY DIFFRACTION96.89
3.07-3.140.35271640.2663066X-RAY DIFFRACTION96.39
3.14-3.210.37771230.27083054X-RAY DIFFRACTION96.68
3.21-3.30.35661440.27213030X-RAY DIFFRACTION96.53
3.3-3.40.28891260.27173104X-RAY DIFFRACTION96.07
3.4-3.510.3097690.28191851X-RAY DIFFRACTION58.59
3.51-3.630.33021960.27352982X-RAY DIFFRACTION95.01
3.63-3.780.39291100.25941816X-RAY DIFFRACTION58.81
3.78-3.950.2941290.23922265X-RAY DIFFRACTION71.29
3.95-4.160.27611230.22383006X-RAY DIFFRACTION95.37
4.16-4.420.26991300.21553044X-RAY DIFFRACTION93.93
4.42-4.760.27181460.21122888X-RAY DIFFRACTION93.35
4.76-5.240.26721550.21852890X-RAY DIFFRACTION92.24
5.24-60.28681730.24132940X-RAY DIFFRACTION93.2
6-7.550.30331610.24672894X-RAY DIFFRACTION91.91
7.55-43.670.23731590.22572836X-RAY DIFFRACTION90.48
Refinement TLS params.Method: refined / Origin x: -34.023895990873 Å / Origin y: 17.935868065036 Å / Origin z: 54.132224100077 Å
111213212223313233
T0.085809611900421 Å2-0.031182201051396 Å2-0.01569343100634 Å2-0.10515994761842 Å20.0037434540673195 Å2--0.096520189719796 Å2
L0.021908055458418 °2-0.00492594594953 °2-0.010584122938662 °2-0.060281464645431 °2-0.02641815182582 °2--0.045394664228188 °2
S-0.062338740622864 Å °-0.0030833600079469 Å °-0.0051178799910069 Å °0.01066194527049 Å °0.092776917076056 Å °0.073117818285781 Å °-0.017609499770203 Å °-0.0184774009361 Å °0.018696116389097 Å °
Refinement TLS groupSelection details: all

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