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- PDB-1n4s: Protein Geranylgeranyltransferase type-I Complexed with GGPP and ... -

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Basic information

Entry
Database: PDB / ID: 1n4s
TitleProtein Geranylgeranyltransferase type-I Complexed with GGPP and a Geranylgeranylated KKKSKTKCVIL Peptide Product
Components
  • Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
  • Geranylgeranyl transferase type-1 subunit beta
  • Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
KeywordsTRANSFERASE / protein geranylgeranyltransferase type-I / GGTase / geranylgeranyl / protein prenylation / CaaX / lipid modification / rap2b
Function / homology
Function and homology information


Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / protein geranylgeranyltransferase type I / positive regulation of tubulin deacetylation / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / protein geranylgeranyltransferase type I / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / : / microtubule associated complex / forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / heterocyclic compound binding / enzyme-linked receptor protein signaling pathway / Rac protein signal transduction / : / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / alpha-tubulin binding / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / glial cell proliferation / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / positive regulation of cell cycle / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / positive regulation of glial cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / homeostasis of number of cells within a tissue / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / Ras activation upon Ca2+ influx through NMDA receptor / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / small monomeric GTPase / VEGFR2 mediated cell proliferation / response to cytokine / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / visual learning / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / G protein activity / receptor tyrosine kinase binding / response to organic cyclic compound
Similarity search - Function
Geranylgeranyl transferase type-1 subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid ...Geranylgeranyl transferase type-1 subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
GERAN-8-YL GERAN / GERANYLGERANYL DIPHOSPHATE / GTPase KRas / Geranylgeranyl transferase type-1 subunit beta / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTaylor, J.S. / Reid, T.S. / Casey, P.J. / Beese, L.S.
CitationJournal: EMBO J. / Year: 2003
Title: Structure of mammalian protein geranylgeranyltransferase type-I
Authors: Taylor, J.S. / Reid, T.S. / Terry, K.L. / Casey, P.J. / Beese, L.S.
History
DepositionNov 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jun 28, 2017Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / struct_ref / struct_ref_seq
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num
Revision 2.0Oct 30, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Geranylgeranyl transferase type-1 subunit beta
C: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
D: Geranylgeranyl transferase type-1 subunit beta
E: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
F: Geranylgeranyl transferase type-1 subunit beta
G: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
H: Geranylgeranyl transferase type-1 subunit beta
I: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
J: Geranylgeranyl transferase type-1 subunit beta
K: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
L: Geranylgeranyl transferase type-1 subunit beta
M: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
N: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
O: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
P: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
Q: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
R: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)532,13145
Polymers527,07018
Non-polymers5,06127
Water23,3471296
1
A: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Geranylgeranyl transferase type-1 subunit beta
M: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6717
Polymers87,8453
Non-polymers8264
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
D: Geranylgeranyl transferase type-1 subunit beta
N: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7068
Polymers87,8453
Non-polymers8615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
F: Geranylgeranyl transferase type-1 subunit beta
O: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6717
Polymers87,8453
Non-polymers8264
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
H: Geranylgeranyl transferase type-1 subunit beta
P: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7068
Polymers87,8453
Non-polymers8615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
J: Geranylgeranyl transferase type-1 subunit beta
Q: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6717
Polymers87,8453
Non-polymers8264
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
L: Geranylgeranyl transferase type-1 subunit beta
R: Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7068
Polymers87,8453
Non-polymers8615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)271.121, 268.426, 184.818
Angle α, β, γ (deg.)90.00, 131.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-1629-

HOH

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Components

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Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / CAAX farnesyltransferase subunit alpha / FTase-alpha / Ras proteins prenyltransferase subunit alpha ...CAAX farnesyltransferase subunit alpha / FTase-alpha / Ras proteins prenyltransferase subunit alpha / Type I protein geranyl-geranyltransferase subunit alpha / GGTase-I-alpha


Mass: 44098.145 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Fnta / Plasmid: ATCC 63134 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I
#2: Protein
Geranylgeranyl transferase type-1 subunit beta / Geranylgeranyl transferase type I subunit beta / GGTase-I-beta / Type I protein geranyl- ...Geranylgeranyl transferase type I subunit beta / GGTase-I-beta / Type I protein geranyl-geranyltransferase subunit beta


Mass: 42466.176 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pggt1b / Plasmid: ATCC 63134 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P53610, protein geranylgeranyltransferase type I

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Protein/peptide , 1 types, 6 molecules MNOPQR

#3: Protein/peptide
Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b / KKKSKTKCVIL Peptide Product


Mass: 1280.685 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE GERANYLGERANYL LIPID WAS ADDED BY THE ENZYME.
Source: (synth.) Homo sapiens (human) / References: UniProt: P01116*PLUS

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Non-polymers , 5 types, 1323 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE


Mass: 450.443 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H36O7P2
#7: Chemical
ChemComp-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H34
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1296 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.77 Å3/Da / Density % sol: 74.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: ammonium sulfate, sodium citrate, dithiothreitol , pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
21.3 Mammonium sulfate1reservoir
3175 mM1reservoirpH6.5Na3 citrate
420 mMdithiothreitol1reservoir
5100 mMMES1reservoirpH6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2002 / Details: Pt-coated toroidal Si mirror
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→29.98 Å / Num. all: 300000 / Num. obs: 300000 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 56.3 Å2 / Rsym value: 0.069 / Net I/σ(I): 13.6
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.43 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 1011902 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
Highest resolution: 2.6 Å / % possible obs: 100 % / Rmerge(I) obs: 0.435

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.98 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: ncs restraints employed during refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.214 14968 5 %RANDOM
Rwork0.194 ---
obs0.194 299339 99.3 %-
all-300000 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7338 Å2 / ksol: 0.358207 e/Å3
Displacement parametersBiso mean: 54 Å2
Baniso -1Baniso -2Baniso -3
1--5.9 Å20 Å2-4.8 Å2
2--11.83 Å20 Å2
3----5.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32319 0 309 1296 33924
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.322.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 2379 4.8 %
Rwork0.286 46914 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMGGPP.TOP
X-RAY DIFFRACTION4GGPP.PARION.TOP
X-RAY DIFFRACTION5GG-CYS.PARGG-CYS.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rfree: 0.315 / Rfactor Rwork: 0.293

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