[English] 日本語
Yorodumi
- PDB-5c1b: p97-delta709-728 in complex with a UFD1-SHP peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c1b
Titlep97-delta709-728 in complex with a UFD1-SHP peptide
Components
  • Transitional endoplasmic reticulum ATPase
  • Ubiquitin fusion degradation protein 1 homolog
KeywordsHYDROLASE / AAA ATPase / ERAD / VCP / CDC48
Function / homology
Function and homology information


UFD1-NPL4 complex / negative regulation of RIG-I signaling pathway / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / cytoplasm protein quality control ...UFD1-NPL4 complex / negative regulation of RIG-I signaling pathway / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / cytoplasm protein quality control / Derlin-1 retrotranslocation complex / protein-DNA covalent cross-linking repair / positive regulation of protein K63-linked deubiquitination / positive regulation of oxidative phosphorylation / mitotic spindle disassembly / deubiquitinase activator activity / NADH metabolic process / aggresome assembly / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / cellular response to misfolded protein / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / negative regulation of type I interferon production / regulation of aerobic respiration / stress granule disassembly / regulation of synapse organization / positive regulation of ATP biosynthetic process / ATPase complex / ubiquitin-specific protease binding / MHC class I protein binding / ubiquitin-like protein ligase binding / : / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / HSF1 activation / translesion synthesis / interstrand cross-link repair / proteasomal protein catabolic process / Protein methylation / ATP metabolic process / endoplasmic reticulum unfolded protein response / negative regulation of smoothened signaling pathway / ERAD pathway / Attachment and Entry / lipid droplet / proteasome complex / viral genome replication / Josephin domain DUBs / skeletal system development / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Hh mutants are degraded by ERAD / positive regulation of protein-containing complex assembly / macroautophagy / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / establishment of protein localization / Translesion Synthesis by POLH / positive regulation of non-canonical NF-kappaB signal transduction / ABC-family proteins mediated transport / ADP binding / autophagy / Aggrephagy / positive regulation of protein catabolic process / cytoplasmic stress granule / azurophil granule lumen / KEAP1-NFE2L2 pathway / Ovarian tumor domain proteases / positive regulation of canonical Wnt signaling pathway / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / site of double-strand break / cellular response to heat / ubiquitin-dependent protein catabolic process / protein phosphatase binding / regulation of apoptotic process / secretory granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / cysteine-type deubiquitinase activity / ficolin-1-rich granule lumen / Attachment and Entry / Ub-specific processing proteases / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair / ubiquitin protein ligase binding / lipid binding / DNA damage response / Neutrophil degranulation / endoplasmic reticulum membrane
Similarity search - Function
Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1 / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Helicase, Ruva Protein; domain 3 - #60 / Cell division protein 48 (CDC48), N-terminal domain ...Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1 / Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Helicase, Ruva Protein; domain 3 - #60 / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / CDC48 domain 2-like superfamily / : / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Transitional endoplasmic reticulum ATPase / Ubiquitin recognition factor in ER-associated degradation protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.08 Å
AuthorsHaenzelmann, P. / Schindelin, H.
CitationJournal: Structure / Year: 2016
Title: Characterization of an Additional Binding Surface on the p97 N-Terminal Domain Involved in Bipartite Cofactor Interactions.
Authors: Hanzelmann, P. / Schindelin, H.
History
DepositionJun 13, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transitional endoplasmic reticulum ATPase
B: Transitional endoplasmic reticulum ATPase
C: Transitional endoplasmic reticulum ATPase
D: Transitional endoplasmic reticulum ATPase
E: Transitional endoplasmic reticulum ATPase
F: Transitional endoplasmic reticulum ATPase
V: Ubiquitin fusion degradation protein 1 homolog
U: Ubiquitin fusion degradation protein 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)532,93940
Polymers525,9718
Non-polymers6,96832
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59670 Å2
ΔGint-405 kcal/mol
Surface area176050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.715, 180.664, 254.958
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide , 2 types, 8 molecules ABCDEFVU

#1: Protein
Transitional endoplasmic reticulum ATPase / TER ATPase / 15S Mg(2+)-ATPase p97 subunit / Valosin-containing protein / VCP


Mass: 86933.094 Da / Num. of mol.: 6 / Mutation: 709-728 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P55072, vesicle-fusing ATPase
#2: Protein/peptide Ubiquitin fusion degradation protein 1 homolog / UB fusion protein 1


Mass: 2186.454 Da / Num. of mol.: 2 / Fragment: UNP residues 221-241 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q92890

-
Non-polymers , 5 types, 62 molecules

#3: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 6.5-7% PEG 4000, 0.4-0.6 M potassium acetate, 0.1 M MES pH 5.75

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.08→49.14 Å / Num. obs: 120596 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 106.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.037 / Net I/σ(I): 12.8 / Num. measured all: 1326505
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.08-3.1310.92.5821.16437259200.5270.81399.9
16.87-49.149.90.04240.681708220.9990.01396.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.1.27data scaling
MxCuBEdata collection
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CF3

3cf3


Resolution: 3.08→49.136 Å / SU ML: 0.4 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 6052 5.02 %
Rwork0.1975 114426 -
obs0.1997 120478 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 575.3 Å2 / Biso mean: 145.5665 Å2 / Biso min: 45.47 Å2
Refinement stepCycle: final / Resolution: 3.08→49.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34227 0 574 30 34831
Biso mean--111.54 126.68 -
Num. residues----4365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00335264
X-RAY DIFFRACTIONf_angle_d0.7347648
X-RAY DIFFRACTIONf_chiral_restr0.045335
X-RAY DIFFRACTIONf_plane_restr0.0036232
X-RAY DIFFRACTIONf_dihedral_angle_d17.06513669
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.08-3.1150.3442280.315237643992
3.115-3.15170.35521950.304337573952
3.1517-3.19010.38581930.284337843977
3.1901-3.23050.32141990.272537823981
3.2305-3.2730.29662020.260237723974
3.273-3.31780.29852060.251137403946
3.3178-3.36520.31391950.239538274022
3.3652-3.41540.29911830.248837743957
3.4154-3.46870.2941800.24537883968
3.4687-3.52560.30652030.226937913994
3.5256-3.58640.25142090.220937513960
3.5864-3.65160.29391800.208438103990
3.6516-3.72180.27751790.220438284007
3.7218-3.79770.25492180.214437623980
3.7977-3.88030.27242070.205637843991
3.8803-3.97050.2561940.194737813975
3.9705-4.06970.22372140.187737874001
4.0697-4.17970.23872120.184138254037
4.1797-4.30260.24492040.18937913995
4.3026-4.44140.22462080.17737823990
4.4414-4.60010.23972090.173238104019
4.6001-4.78410.21361920.170538344026
4.7841-5.00160.22831950.175338384033
5.0016-5.2650.20971880.184338244012
5.265-5.59450.2552220.204438474069
5.5945-6.02570.26491840.217238614045
6.0257-6.63080.25042110.209338494060
6.6308-7.58730.24832000.194438944094
7.5873-9.54770.17962070.157839384145
9.5477-49.14210.20842350.192140514286
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)
14.0973-2.16370.53934.6444-0.42124.72080.12470.48650.52230.2391-0.08810.97680.2227-1.4896-0.00270.7897-0.13260.211.7338-0.03781.5091-52.24786.032361.7124
26.60762.9840.93553.51321.50785.46960.3537-0.56930.00810.4541-0.40510.27460.2567-0.2560.0580.5857-0.02870.06690.73750.15930.7663-22.22766.444361.2616
31.6537-1.19640.29451.6906-1.01312.0702-0.0910.1588-0.1813-0.20840.13410.33210.5152-0.5189-0.05850.9337-0.251-0.03410.78620.10040.8894-15.3548-27.159852.1903
43.2653-0.9532.01571.1863-0.41425.59860.05650.45260.3134-0.5792-0.12490.4314-0.1325-0.68070.06690.9063-0.0037-0.17070.9910.24430.9981-25.27919.099614.4689
54.3399-0.2824-1.18131.7167-0.15236.46690.12960.42510.0301-0.2958-0.0811-0.06490.6903-0.3176-0.11030.6440.064-0.00270.54390.18620.718-7.396613.104224.8685
62.3857-0.185-0.56461.6915-0.27161.8681-0.13590.5625-0.3346-0.13110-0.00190.452-0.2170.11630.9887-0.1780.02250.82190.00110.6444-0.9251-21.026222.5352
71.49271.3519-1.7142.1628-2.77195.103-0.16550.40990.146-0.8147-0.1267-0.40620.02490.19350.26111.04150.02910.16890.79890.20580.8826.154633.0457.5312
84.0784-0.2231-0.78182.3842-0.71043.9677-0.1290.1533-0.3879-0.2009-0.2522-0.56320.23140.60550.34880.67290.08480.06840.59110.15420.692526.81221.460425.7349
93.57310.35860.31092.1915-0.27841.12060.10510.7733-0.1685-0.23960.0422-0.52710.35020.471-0.13480.990.09560.17171.055-0.03320.888531.8881-11.896419.7773
103.3380.96273.04296.65852.04884.9373-0.0069-0.11590.4434-0.2276-0.1285-0.7854-0.74420.73380.12761.1244-0.4080.0451.03480.14821.56967.661338.758251.8272
115.591-0.75280.72451.9672-1.2875.48590.1990.4520.0241-0.1228-0.3245-0.4557-0.27470.20960.11280.6503-0.0887-0.01180.55170.10980.916939.403625.092647.3101
121.73880.69140.00022.22060.18491.85340.1845-0.1066-0.26190.0011-0.2913-0.7070.17960.53780.10550.59280.0518-0.01591.01350.21781.170352.2139-6.682751.1382
132.7024-0.20412.04180.6084-0.11857.1506-0.1544-0.14170.38430.33050.0433-0.2081-0.71010.7490.13960.9835-0.1234-0.12530.84640.03540.8238.942824.450492.5378
140.57270.24740.01992.16770.8720.98030.1362-0.422-0.44410.6202-0.164-0.31180.2617-0.00970.03460.9039-0.1187-0.24880.88550.30571.038235.8293-13.616483.1572
152.5404-0.3076-2.85363.51413.14795.31670.5368-1.39870.2491.1743-0.56240.55361.0464-1.83740.01251.8889-0.62350.38332.8752-0.01821.2634-15.71336.3675112.9705
165.66283.1875-0.08265.84920.00475.57360.3796-0.43920.03960.504-0.24270.07420.5028-0.0126-0.09270.7575-0.10350.00980.92270.0950.54872.69619.451287.1854
173.7697-2.9484-0.58173.01480.26510.78690.0128-0.1238-0.04110.5734-0.06150.1564-0.0177-0.31630.06891.097-0.28190.00850.72440.10880.7893-2.0574-15.182785.6753
186.73163.0364-1.47414.204-0.98562.7919-0.07870.3104-0.13220.23980.0964-0.0948-0.05320.0048-0.03070.75920.0115-0.07380.48870.11450.65314.7418-33.876778.0978
192.1475-2.0167-1.71232.54222.49722.60420.1479-0.7647-0.4211.80480.133-1.247-0.16460.3194-0.0942.1729-0.5716-0.16661.91580.06422.282872.78350.887568.309
209.87110.3285-1.59416.3655-0.91936.92540.0601-0.1179-0.1413-1.30590.81720.5225-0.81480.1012-0.74461.46881.0393-0.15733.1281-0.1431.2391-64.389317.16548.373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 209 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 210 through 433 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 434 through 770 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 21 through 295 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 296 through 448 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 449 through 770 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 21 through 295 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 296 through 448 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 449 through 770 )C0
10X-RAY DIFFRACTION10chain 'D' and (resid 21 through 209 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 210 through 407 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 408 through 770 )D0
13X-RAY DIFFRACTION13chain 'E' and (resid 21 through 364 )E0
14X-RAY DIFFRACTION14chain 'E' and (resid 365 through 770 )E0
15X-RAY DIFFRACTION15chain 'F' and (resid 21 through 209 )F0
16X-RAY DIFFRACTION16chain 'F' and (resid 210 through 407 )F0
17X-RAY DIFFRACTION17chain 'F' and (resid 408 through 568 )F0
18X-RAY DIFFRACTION18chain 'F' and (resid 569 through 770 )F0
19X-RAY DIFFRACTION19chain 'V' and (resid 225 through 235 )V0
20X-RAY DIFFRACTION20chain 'U' and (resid 226 through 235 )U0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more