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- PDB-4kln: Structure of p97 N-D1 A232E mutant in complex with ATPgS -

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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


positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex ...positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / BAT3 complex binding / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / aggresome assembly / regulation of protein localization to chromatin / NADH metabolic process / vesicle-fusing ATPase / cellular response to misfolded protein / : / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / ERAD pathway / ubiquitin-modified protein reader activity / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / ATPase complex / regulation of synapse organization / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / autophagosome maturation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / HSF1 activation / translesion synthesis / endoplasmic reticulum to Golgi vesicle-mediated transport / MHC class I protein binding / Protein methylation / negative regulation of smoothened signaling pathway / interstrand cross-link repair / Attachment and Entry / : / ATP metabolic process / endoplasmic reticulum unfolded protein response / proteasome complex / lipid droplet / viral genome replication / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ADP binding / proteasomal protein catabolic process / Hh mutants are degraded by ERAD / positive regulation of protein-containing complex assembly / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / macroautophagy / Translesion Synthesis by POLH / ABC-family proteins mediated transport / establishment of protein localization / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / cellular response to heat / Neddylation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein phosphatase binding / regulation of apoptotic process / secretory granule lumen / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / protein domain specific binding / DNA repair / intracellular membrane-bounded organelle / lipid binding / glutamatergic synapse / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / 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 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 ...Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / Barwin-like endoglucanases - #20 / Helicase, Ruva Protein; domain 3 - #60 / AAA ATPase, CDC48 family / Barwin-like endoglucanases / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 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

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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

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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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)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

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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

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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

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