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- PDB-4ylq: Crystal Structure of a FVIIa-Trypsin Chimera (FT) in Complex with... -

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Basic information

Entry
Database: PDB / ID: 4ylq
TitleCrystal Structure of a FVIIa-Trypsin Chimera (FT) in Complex with Soluble Tissue Factor
Components
  • (Coagulation factor ...) x 2
  • Tissue factor
KeywordsHYDROLASE / trypsin-fold / protein-protein complex
Function / homology
Function and homology information


activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / 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 / response to genistein / serine-type peptidase complex ...activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / 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 / response to genistein / serine-type peptidase complex / response to vitamin K / positive regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of leukocyte chemotaxis / response to thyroxine / NGF-stimulated transcription / response to cholesterol / cytokine receptor activity / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of endothelial cell apoptotic process / 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 / positive regulation of endothelial cell proliferation / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian expression / positive regulation of interleukin-8 production / circadian rhythm / protein processing / phospholipid binding / Golgi lumen / response to estrogen / positive regulation of angiogenesis / cytokine-mediated signaling pathway / blood coagulation / response to estradiol / : / protease binding / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / signaling receptor binding / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / positive regulation of gene expression / cell surface / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily ...Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / 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 / Fibronectin type III / Fibronectin type III 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 / Trypsin-like serine proteases / Thrombin, subunit H / Immunoglobulin-like fold / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-0Z7 / alpha-L-fucopyranose / N-PROPANOL / TETRAMETHYLAMMONIUM ION / Coagulation factor VII / Tissue factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
Model detailsA human-FVIIa Variant with the 170-loop swapped with that from human-Trypsin, and an additional ...A human-FVIIa Variant with the 170-loop swapped with that from human-Trypsin, and an additional replacement of Tyr170b with Phe
AuthorsSorensen, A.B. / Svensson, L.A. / Gandhi, P.S.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Molecular Basis of Enhanced Activity in Factor VIIa-Trypsin Variants Conveys Insights into Tissue Factor-mediated Allosteric Regulation of Factor VIIa Activity.
Authors: Sorensen, A.B. / Madsen, J.J. / Svensson, L.A. / Pedersen, A.A. / stergaard, H. / Overgaard, M.T. / Olsen, O.H. / Gandhi, P.S.
History
DepositionMar 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Mar 9, 2016Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 16, 2019Group: Data collection / Category: chem_comp / reflns_shell / Item: _chem_comp.type
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / diffrn_radiation_wavelength / entity / entity_name_com / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity_name_com.entity_id / _entity_src_gen.entity_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Coagulation factor VII
H: Coagulation factor VII
T: Tissue factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,02938
Polymers69,8223
Non-polymers3,20735
Water10,359575
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12850 Å2
ΔGint-1 kcal/mol
Surface area26470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.310, 80.040, 123.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Coagulation factor ... , 2 types, 2 molecules LH

#1: Protein Coagulation factor VII / Proconvertin / Serum prothrombin conversion accelerator / SPCA


Mass: 17487.076 Da / Num. of mol.: 1
Fragment: BLOOD COAGULATION FACTOR VIIA LIGHT CHAIN, UNP residues 61-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: F7 / Organ: Kidney / Plasmid: pQMCF-5
Details (production host): Cells were licensed from Icosagen (Estonia)
Cell line (production host): CHOEBNALT85 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa
#2: Protein Coagulation factor VII / Proconvertin / Serum prothrombin conversion accelerator / SPCA


Mass: 27508.611 Da / Num. of mol.: 1 / Fragment: UNP residues 213-466 / Mutation: [169-175] LQQSRKVGDSPN - EASFPGK
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: F7 / Organ: Kidney / Plasmid: pQMCF-5
Details (production host): Cells were licensed from Icosagen (Estonia)
Cell line (production host): CHOEBNALT85 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P08709, coagulation factor VIIa

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Protein , 1 types, 1 molecules T

#3: Protein Tissue factor / TF / Coagulation factor III / Thromboplastin


Mass: 24826.512 Da / Num. of mol.: 1 / Fragment: UNP residues 33-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: F3 / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami 2 / References: UniProt: P13726

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-D-xylopyranose-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 444.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-3DXylpa1-3DGlcpb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a212h-1a_1-5]/1-2-2/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][b-D-Glcp]{[(3+1)][a-D-Xylp]{[(3+1)][a-D-Xylp]{}}}}LINUCSPDB-CARE
#6: 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.: 1
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 5 types, 608 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#7: Chemical...
ChemComp-TMA / TETRAMETHYLAMMONIUM ION


Mass: 74.145 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Formula: C4H12N
#8: Chemical ChemComp-0Z7 / N-acetyl-D-phenylalanyl-N-[(2S,3S)-6-carbamimidamido-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide / Proconvertin / Serum prothrombin conversion accelerator / SPCA


Mass: 546.081 Da / Num. of mol.: 1 / Fragment: UNP residues 213-466 / Mutation: [169-175] LQQSRKVGDSPN - EASFPGK
Source method: isolated from a genetically manipulated source
Formula: C27H38ClN6O4 / Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: F7 / Organ: Kidney / Plasmid: pQMCF-5
Details (production host): Cells were licensed from Icosagen (Estonia)
Cell line (production host): CHOEBNALT85 / Production host: Cricetulus griseus (Chinese hamster) / References: coagulation factor VIIa
#9: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.23 % / Description: Elongated hexgonal prisms
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M NaCitrate, 16.6% PEG 3350, 12.5% 1-Propanol, with seeding

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2014
Details: Rh-coated Si mirrors: M1 collimating mirror, M2 toroidal focusing mirror
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→33.57 Å / Num. all: 138932 / Num. obs: 138932 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 15.27 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.101 / Χ2: 1.007 / Net I/σ(I): 14.07 / Num. measured all: 1011012
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.4-1.456.10.2642.0740.838235113778137642.27599.9
1.45-1.50.4451.6181.258614212013120111.745100
1.5-1.550.621.1941.747673610505105011.286100
1.55-1.60.7560.8782.3668216929692960.945100
1.6-20.9720.3166.5133480345335453200.34100
2-2.50.9960.09720.3317313423393233890.104100
2.5-30.9990.05432.737615110429104270.058100
3-40.9990.03347.9459284837683700.03599.9
4-60.9990.02859.135210438043780.03100
6-1010.03262.3715237150415040.034100
100.9990.02666.3137484594390.02895.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.26 Å40.31 Å
Translation7.26 Å40.31 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSMarch 30, 2013data reduction
XSCALEJuly 4, 2012 BUILT=20130706data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In-House FVIIa-WT:sTF-FFR similar to 1DAN

1dan


Resolution: 1.4→34.253 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1737 6917 4.98 %Random selection
Rwork0.1397 132015 --
obs0.1414 138932 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.64 Å2 / Biso mean: 26.4558 Å2 / Biso min: 7.7 Å2
Refinement stepCycle: final / Resolution: 1.4→34.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4732 0 469 575 5776
Biso mean--53.85 33.19 -
Num. residues----603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0235143
X-RAY DIFFRACTIONf_angle_d1.7616957
X-RAY DIFFRACTIONf_chiral_restr0.112763
X-RAY DIFFRACTIONf_plane_restr0.01876
X-RAY DIFFRACTIONf_dihedral_angle_d14.2061817
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.41590.37692140.34464143435796
1.4159-1.43260.36442290.306743844613100
1.4326-1.450.30192210.284843624583100
1.45-1.46840.31552110.26143654576100
1.4684-1.48770.28082450.247743864631100
1.4877-1.50810.26832190.227943524571100
1.5081-1.52960.27592250.221843574582100
1.5296-1.55250.23962320.200843994631100
1.5525-1.57670.2522020.191643664568100
1.5767-1.60260.25362170.178644074624100
1.6026-1.63020.22712180.16443444562100
1.6302-1.65990.20222250.15643854610100
1.6599-1.69180.18812290.145244094638100
1.6918-1.72630.19762140.132443574571100
1.7263-1.76390.16542170.124743954612100
1.7639-1.80490.16722210.122243974618100
1.8049-1.850.16782540.121143754629100
1.85-1.90.16552370.118643994636100
1.9-1.95590.16832210.116543954616100
1.9559-2.01910.1482290.113544004629100
2.0191-2.09120.15512350.112744094644100
2.0912-2.17490.15522360.111843884624100
2.1749-2.27390.1522730.110743934666100
2.2739-2.39380.15392580.115443854643100
2.3938-2.54370.17212320.122844624694100
2.5437-2.740.16362470.126344254672100
2.74-3.01560.16762330.13144534686100
3.0156-3.45160.1462420.128444714713100
3.4516-4.34730.14022400.126545274767100
4.3473-34.26360.16442410.146247254966100

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