[English] 日本語
Yorodumi
- PDB-4kln: Structure of p97 N-D1 A232E mutant in complex with ATPgS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4kln
TitleStructure of p97 N-D1 A232E mutant in complex with ATPgS
ComponentsTransitional endoplasmic reticulum ATPase
KeywordsHYDROLASE / Transport protein
Function / homology
Function and homology information


: / 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 / BAT3 complex binding / cellular response to arsenite ion / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination ...: / 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 / BAT3 complex binding / cellular response to arsenite ion / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / cytoplasm protein quality control / positive regulation of oxidative phosphorylation / : / aggresome assembly / deubiquitinase activator activity / mitotic spindle disassembly / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / VCP-NPL4-UFD1 AAA ATPase complex / cellular response to misfolded protein / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / stress granule disassembly / ATPase complex / regulation of synapse organization / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / 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 / HSF1 activation / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / ATP metabolic process / endoplasmic reticulum unfolded protein response / proteasomal protein catabolic process / Protein methylation / Attachment and Entry / ERAD pathway / lipid droplet / proteasome complex / viral genome replication / Josephin domain DUBs / negative regulation of smoothened signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / macroautophagy / establishment of protein localization / Hh mutants are degraded by ERAD / positive regulation of protein-containing complex assembly / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / positive regulation of non-canonical NF-kappaB signal transduction / Translesion Synthesis by POLH / ADP binding / ABC-family proteins mediated transport / autophagy / cytoplasmic stress granule / Aggrephagy / positive regulation of protein catabolic process / azurophil granule lumen / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / 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 / cellular response to heat / site of double-strand break / Neddylation / ubiquitin-dependent protein catabolic process / secretory granule lumen / protein phosphatase binding / regulation of apoptotic process / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / Attachment and Entry / protein ubiquitination / ciliary basal body / protein domain specific binding / DNA repair / intracellular membrane-bounded organelle / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / lipid binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / glutamatergic synapse / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / RNA binding
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / : / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain ...Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsXia, D. / Tang, W.K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Altered Intersubunit Communication Is the Molecular Basis for Functional Defects of Pathogenic p97 Mutants.
Authors: Tang, W.K. / Xia, D.
History
DepositionMay 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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 / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,12118
Polymers327,8366
Non-polymers3,28512
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22790 Å2
ΔGint-70 kcal/mol
Surface area122270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.147, 104.514, 109.528
Angle α, β, γ (deg.)98.11, 90.55, 92.72
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.681715, 0.607227, 0.408094), (-0.239873, 0.712473, -0.659426), (-0.691177, 0.35165, 0.631361)-2.09626, 7.11983, 8.02905
3given(0.041559, 0.9919, 0.120028), (0.144986, 0.112873, -0.982974), (-0.988561, 0.058254, -0.139121)6.10384, 9.59427, 14.99959
4given(-0.183084, 0.745886, -0.640417), (0.735389, -0.328421, -0.592742), (-0.652444, -0.579477, -0.488388)8.34296, 4.67957, 19.86972
5given(0.090384, 0.180877, -0.979344), (0.995502, 0.01165, 0.094026), (0.028416, -0.983437, -0.179011)13.264, -3.65246, 13.96596
6given(0.753269, -0.222638, -0.618885), (0.580843, 0.666624, 0.467154), (0.308557, -0.711368, 0.631465)3.5898, -6.26068, 5.37556

-
Components

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


Mass: 54639.344 Da / Num. of mol.: 6 / Fragment: UNP residue 1-481 / Mutation: A232E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: human / Gene: p97, VCP / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P55072, vesicle-fusing ATPase
#2: 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.: 6 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1M citrate, pH 5.8, 0.3M NaCl, 13.6% PEG 3350, 20% glycerol, 0.525% benzamidine, VAPOR DIFFUSION, SITTING DROP, temperature 288K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 7, 2010
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 99906 / % possible obs: 83.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.6→2.69 Å / % possible all: 71.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→46.29 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.925 / SU B: 43.205 / SU ML: 0.377 / Cross valid method: THROUGHOUT / ESU R: 1.222 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28893 4959 5 %RANDOM
Rwork0.27425 ---
obs0.27497 94946 83.11 %-
all-260257 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.242 Å2
Baniso -1Baniso -2Baniso -3
1-7.4 Å27.38 Å2-2.51 Å2
2---2.89 Å2-1.49 Å2
3----4.41 Å2
Refinement stepCycle: LAST / Resolution: 2.62→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21198 0 192 166 21556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01921720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1221.99729388
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53152700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27724.2511002
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.196154002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.51915198
X-RAY DIFFRACTIONr_chiral_restr0.0730.23354
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02116200
X-RAY DIFFRACTIONr_gen_planes_other
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_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.501 218 -
Rwork0.522 4500 -
obs--53.01 %
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)
10.89360.42380.39522.9209-3.24634.5178-0.05240.00790.11790.50360.40340.401-0.6538-0.523-0.3510.2060.04540.21630.12870.06040.3533-2.20880.12282.1881
20.1628-0.2045-0.23623.0356-1.72743.21450.01220.11340.1127-0.08550.04470.1202-0.0875-0.0924-0.05690.0537-0.07260.04620.2130.05250.31377.173674.6941-9.8603
31.1672-0.0760.78970.3503-0.05581.1327-0.04820.1359-0.0450.10830.05690.08120.0489-0.0424-0.00880.1679-0.19510.10050.39880.02940.4375.840848.8014-4.3622
41.6136-1.4094-2.54052.40933.16584.77890.06360.355-0.217-0.2099-0.1065-0.0629-0.2766-0.35620.04290.1927-0.27120.05610.63170.09710.6373-13.532149.8828-51.8441
51.9003-1.27540.33194.519-2.00886.8394-0.0193-0.0242-0.1121-0.2633-0.02450.06640.31570.04090.04370.1088-0.16250.04970.3780.01360.31096.303448.1409-62.3096
61.5072-1.12860.08292.01050.47531.7134-0.0764-0.0472-0.05790.04670.154-0.0934-0.1578-0.153-0.07750.0983-0.09920.02750.26540.04630.23135.933640.9067-23.7106
71.5846-1.58780.17892.23831.3023.8895-0.04160.1358-0.2803-0.0479-0.07690.38930.0009-0.32880.11850.1485-0.24750.06920.49060.00940.54-4.52915.8505-44.8647
85.6781-2.0936-0.58191.9382-0.56223.26510.02280.1503-0.7185-0.3441-0.0312-0.1306-0.4983-0.62460.00840.5826-0.17630.16490.48460.00930.37622.5489-1.0283-68.5206
95.32730.31742.75342.3801-1.8915.0055-0.03060.16870.1544-0.29010.1126-0.3474-0.05840.5506-0.0820.2887-0.18390.2170.2253-0.16410.290843.70885.9761-65.5121
101.2826-0.76450.17322.05190.18550.4701-0.03820.0085-0.0339-0.07940.0421-0.1086-0.1005-0.1933-0.00390.186-0.180.03890.40640.01080.323118.746316.295-37.9764
113.5068-1.0627-0.4221.82571.10311.8034-0.08910.117-0.25280.12750.17650.1510.3930.1013-0.08740.2344-0.16510.01450.2640.00510.298830.7498-16.0224-36.7613
128.2340.519-2.20491.5408-0.2091.28280.39950.6839-1.1611-0.138-0.3635-0.32130.08270.0691-0.0360.09040.1409-0.10470.2457-0.14320.466568.9147-22.3643-29.2962
136.0538-0.87810.46133.85573.40987.25620.49570.37020.0839-0.1962-0.1788-0.6226-0.37460.2181-0.31690.07720.03520.05940.10440.15710.353181.7596-4.4424-24.8328
140.4031-0.32540.39361.52450.41961.84790.0340.0279-0.133-0.2291-0.1940.0737-0.2928-0.13890.160.2025-0.14420.02690.3543-0.04360.411442.68081.1932-24.6393
153.3710.43540.83433.4333-0.18381.0589-0.0232-0.2341-0.119-0.05770.0804-0.13040.4576-0.0402-0.05720.2995-0.02970.05520.1097-0.01470.181857.6776-12.81152.9996
162.38512.88480.4623.99380.67121.41750.41790.2894-0.88320.85420.2682-1.36090.19290.3053-0.68610.30370.0366-0.37230.2057-0.19210.658281.61789.786225.1209
178.86570.31930.45638.22162.994.8423-0.39190.8768-0.2626-0.51690.6245-0.5378-0.54930.3435-0.23260.112-0.14340.03450.25-0.05110.075982.673931.867120.9427
181.2663-1.2046-0.20762.06550.55251.57520.0670.0854-0.0111-0.1281-0.018-0.01250.05950.0111-0.04890.096-0.13570.02640.26310.0430.332554.304811.17242.6649
191.6514-1.50250.43433.2917-1.03822.6005-0.2807-0.20880.23410.55160.1373-0.23590.21810.09410.14340.2267-0.0758-0.02490.27950.00110.311749.418222.217435.0075
201.1561-0.18450.39133.9956-0.72421.53410.0490.00570.09070.24610.067-0.3782-0.4117-0.0697-0.1160.1991-0.06010.06750.1077-0.02560.103544.909962.864832.5456
211.4519-1.14790.38062.02390.30292.95820.00360.15890.11670.00220.0133-0.03280.26150.1852-0.01690.1641-0.2250.05220.45590.02050.46440.654235.497912.7463
220.7618-0.5037-0.70021.22881.1731.21010.0129-0.0168-0.1127-0.0765-0.07550.0235-0.0927-0.01320.06270.1961-0.25350.06490.39790.04440.454613.936653.532827.3626
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 107
2X-RAY DIFFRACTION2A108 - 239
3X-RAY DIFFRACTION3A240 - 462
4X-RAY DIFFRACTION3A800 - 801
5X-RAY DIFFRACTION3A901 - 903
6X-RAY DIFFRACTION4B12 - 107
7X-RAY DIFFRACTION5B108 - 200
8X-RAY DIFFRACTION6B201 - 371
9X-RAY DIFFRACTION7B372 - 462
10X-RAY DIFFRACTION7B800 - 801
11X-RAY DIFFRACTION7B901 - 903
12X-RAY DIFFRACTION8C12 - 107
13X-RAY DIFFRACTION9C108 - 200
14X-RAY DIFFRACTION10C201 - 371
15X-RAY DIFFRACTION11C372 - 462
16X-RAY DIFFRACTION11C800 - 801
17X-RAY DIFFRACTION11C901 - 903
18X-RAY DIFFRACTION12D12 - 107
19X-RAY DIFFRACTION13D108 - 200
20X-RAY DIFFRACTION14D201 - 371
21X-RAY DIFFRACTION15D372 - 462
22X-RAY DIFFRACTION15D800 - 801
23X-RAY DIFFRACTION15D901 - 903
24X-RAY DIFFRACTION16E12 - 107
25X-RAY DIFFRACTION17E108 - 200
26X-RAY DIFFRACTION18E201 - 371
27X-RAY DIFFRACTION19E372 - 462
28X-RAY DIFFRACTION19E800 - 801
29X-RAY DIFFRACTION19E901 - 903
30X-RAY DIFFRACTION20F12 - 239
31X-RAY DIFFRACTION21F240 - 371
32X-RAY DIFFRACTION22F372 - 462
33X-RAY DIFFRACTION22F800 - 801
34X-RAY DIFFRACTION22F901 - 903

+
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