[English] 日本語
Yorodumi
- PDB-5dyi: Structure of p97 N-D1 wild-type in complex with ADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dyi
TitleStructure of p97 N-D1 wild-type in complex with ADP
ComponentsTransitional endoplasmic reticulum ATPase
KeywordsHYDROLASE / VCP / AAA ATPase
Function / homology
Function and homology information


positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of protein K63-linked deubiquitination / protein-DNA covalent cross-linking repair / positive regulation of oxidative phosphorylation / ATPase complex / VCP-NSFL1C complex / deubiquitinase activator activity / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion ...positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of protein K63-linked deubiquitination / protein-DNA covalent cross-linking repair / positive regulation of oxidative phosphorylation / ATPase complex / VCP-NSFL1C complex / deubiquitinase activator activity / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion / endoplasmic reticulum stress-induced pre-emptive quality control / Derlin-1 retrotranslocation complex / BAT3 complex binding / ERAD pathway / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / NADH metabolic process / aggresome assembly / vesicle-fusing ATPase / regulation of protein localization to chromatin / ER-associated misfolded protein catabolic process / K48-linked polyubiquitin modification-dependent protein binding / stress granule disassembly / positive regulation of mitochondrial membrane potential / retrograde protein transport, ER to cytosol / autophagosome maturation / regulation of aerobic respiration / MHC class I protein binding / regulation of synapse organization / positive regulation of ATP biosynthetic process / negative regulation of smoothened signaling pathway / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / ATP metabolic process / RHOH GTPase cycle / Attachment and Entry / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / endoplasmic reticulum to Golgi vesicle-mediated transport / Protein methylation / translesion synthesis / HSF1 activation / proteasome complex / interstrand cross-link repair / endoplasmic reticulum unfolded protein response / lipid droplet / ubiquitin-dependent ERAD pathway / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / macroautophagy / ADP binding / Hh mutants are degraded by ERAD / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / Translesion Synthesis by POLH / ABC-family proteins mediated transport / positive regulation of protein catabolic process / positive regulation of protein-containing complex assembly / double-strand break repair / establishment of protein localization / Aggrephagy / cytoplasmic stress granule / autophagy / positive regulation of canonical Wnt signaling pathway / azurophil granule lumen / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / viral genome replication / Ovarian tumor domain proteases / Attachment and Entry / E3 ubiquitin ligases ubiquitinate target proteins / proteasome-mediated ubiquitin-dependent protein catabolic process / cellular response to heat / secretory granule lumen / protein phosphatase binding / regulation of apoptotic process / protein ubiquitination / ficolin-1-rich granule lumen / lipid binding / : / glutamatergic synapse / DNA repair / protein domain specific binding / intracellular membrane-bounded organelle / cellular response to DNA damage stimulus / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / AAA ATPase, CDC48 family / Barwin-like endoglucanases - #20 / 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 ...Vcp-like ATPase; Chain A, domain 2 - #10 / Vcp-like ATPase; Chain A, domain 2 / AAA ATPase, CDC48 family / Barwin-like endoglucanases - #20 / 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 / Helicase, Ruva Protein; domain 3 - #60 / Vps4 C terminal oligomerisation domain / Vps4 oligomerisation, C-terminal / Barwin-like endoglucanases / Aspartate decarboxylase-like domain superfamily / AAA+ lid domain / AAA ATPase, AAA+ lid domain / AAA-protein family signature. / ATPase, AAA-type, conserved site / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleotide triphosphate hydrolases / 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
ADENOSINE-5'-DIPHOSPHATE / Transitional endoplasmic reticulum ATPase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.71 Å
AuthorsTang, W.K. / Xia, D.
CitationJournal: Sci Rep / Year: 2016
Title: Role of the D1-D2 Linker of Human VCP/p97 in the Asymmetry and ATPase Activity of the D1-domain.
Authors: Tang, W.K. / Xia, D.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release

-
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
G: Transitional endoplasmic reticulum ATPase
H: Transitional endoplasmic reticulum ATPase
I: Transitional endoplasmic reticulum ATPase
J: Transitional endoplasmic reticulum ATPase
K: Transitional endoplasmic reticulum ATPase
L: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)660,10224
Polymers654,97612
Non-polymers5,12612
Water0
1
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)330,05112
Polymers327,4886
Non-polymers2,5636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23910 Å2
ΔGint-113 kcal/mol
Surface area110050 Å2
MethodPISA
2
G: Transitional endoplasmic reticulum ATPase
H: Transitional endoplasmic reticulum ATPase
I: Transitional endoplasmic reticulum ATPase
J: Transitional endoplasmic reticulum ATPase
K: Transitional endoplasmic reticulum ATPase
L: Transitional endoplasmic reticulum ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,05112
Polymers327,4886
Non-polymers2,5636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24030 Å2
ΔGint-110 kcal/mol
Surface area110040 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)146.440, 176.210, 256.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111L
121K
12A
22B
32C
42D
52E
62F
72G
82H
92I
102J
112K
122L
13A
23B
33C
43D
53E
63F
73G
83H
93I
103J
113K
123L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A21 - 63
2111B21 - 63
3111C21 - 63
4111D21 - 63
5111E21 - 63
6111F21 - 63
7111G21 - 63
8111H21 - 63
9111I21 - 63
10111J21 - 63
11111L21 - 63
12111K21 - 63
1211A114 - 147
2211B114 - 147
3211C114 - 147
4211D114 - 147
5211E114 - 147
6211F114 - 147
7211G114 - 147
8211H114 - 147
9211I114 - 147
10211J114 - 147
11211L114 - 147
12211K114 - 147
1311A149 - 199
2311B149 - 199
3311C149 - 199
4311D149 - 199
5311E149 - 199
6311F149 - 199
7311G149 - 199
8311H149 - 199
9311I149 - 199
10311J149 - 199
11311L149 - 199
12311K149 - 199
1411A65 - 112
2411B65 - 112
3411C65 - 112
4411D65 - 112
5411E65 - 112
6411F65 - 112
7411G65 - 112
8411H65 - 112
9411I65 - 112
10411J65 - 112
11411L65 - 112
12411K65 - 112
1121A200 - 209
2121B200 - 209
3121C200 - 209
4121D200 - 209
5121E200 - 209
6121F200 - 209
7121G200 - 209
8121H200 - 209
9121I200 - 209
10121J200 - 209
11121K200 - 209
12121L200 - 209
1221A212 - 370
2221B212 - 370
3221C212 - 370
4221D212 - 370
5221E212 - 370
6221F212 - 370
7221G212 - 370
8221H212 - 370
9221I212 - 370
10221J212 - 370
11221K212 - 370
12221L212 - 370
1131A371 - 403
2131B371 - 403
3131C371 - 403
4131D371 - 403
5131E371 - 403
6131F371 - 403
7131G371 - 403
8131H371 - 403
9131I371 - 403
10131J371 - 403
11131K371 - 403
12131L371 - 403
1231A407 - 800
2231B407 - 800
3231C407 - 800
4231D407 - 800
5231E407 - 800
6231F407 - 800
7231G407 - 800
8231H407 - 800
9231I407 - 800
10231J407 - 800
11231K407 - 800
12231L407 - 800

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.551987, -0.050203, 0.83234), (-0.175118, 0.968946, 0.174576), (-0.815257, -0.242121, 0.526054)-81.46857, -20.73938, -21.47482
3given(-0.439546, -0.206886, 0.874069), (-0.344894, 0.937391, 0.048436), (-0.829366, -0.280172, -0.48338)-138.511, -20.15041, 45.8543
4given(-0.980484, -0.196504, -0.00611), (-0.195622, 0.978237, -0.069165), (0.019568, -0.06662, -0.997587)-100.12651, -0.71625, 134.61647
5given(-0.491803, -0.240156, -0.836932), (-0.131331, 0.970673, -0.20136), (0.860745, 0.010886, -0.50892)-24.78069, 6.152, 141.73474
6given(0.491615, -0.157791, -0.856398), (0.048246, 0.986871, -0.154135), (0.869475, 0.034457, 0.492774)25.46204, 10.92739, 74.65029
7given(-0.92801, -0.052511, 0.368835), (0.093444, -0.991178, 0.093995), (0.360646, 0.121694, 0.92473)-108.56269, -93.65288, 30.77656
8given(-0.15097, 0.087191, 0.984686), (0.250292, -0.960274, 0.123403), (0.956327, 0.265089, 0.12315)-108.02319, -89.0003, 108.84141
9given(0.734534, 0.31259, 0.602285), (0.408954, -0.912204, -0.025313), (0.541494, 0.2649, -0.79788)-40.78196, -71.17594, 146.47615
10given(0.887192, 0.237236, -0.395738), (0.245141, -0.968982, -0.031308), (-0.390891, -0.069236, -0.917829)23.63136, -78.64913, 105.62397
11given(-0.776637, 0.076527, -0.625283), (-0.091125, -0.995802, -0.008691), (-0.623322, 0.050229, 0.78035)-38.56246, -97.86588, -5.34829
12given(0.119378, 0.16116, -0.979682), (0.063422, -0.985961, -0.154465), (-0.990821, -0.043694, -0.127923)24.0239, -81.8044, 32.02054
13given(1), (1), (1)
14given(0.513883, -0.02138, 0.857594), (-0.163624, 0.978894, 0.12245), (-0.842111, -0.203249, 0.499539)-81.90866, -15.56269, -16.461
15given(-0.459153, -0.194604, 0.86678), (-0.290206, 0.955038, 0.06069), (-0.839618, -0.223679, -0.494983)-137.57318, -18.13224, 50.84983
16given(-0.969504, -0.244669, 0.014106), (-0.245071, 0.968205, -0.050198), (-0.001376, -0.052124, -0.99864)-104.53783, -7.25985, 134.13371
17given(-0.481962, -0.18964, -0.855423), (-0.136829, 0.980609, -0.1403), (0.865442, 0.049427, -0.498565)-19.00977, 3.37332, 144.70621
18given(0.511282, -0.127779, -0.849861), (0.018501, 0.990292, -0.137763), (0.859214, 0.054712, 0.508683)28.43859, 9.19388, 75.51876
19given(-0.919818, -0.043631, 0.389911), (0.077573, -0.994403, 0.071725), (0.3846, 0.096221, 0.918055)-108.50462, -94.26031, 32.41102
20given(-0.12801, 0.059141, 0.990008), (0.23664, -0.967568, 0.088398), (0.963128, 0.245591, 0.109864)-107.79413, -87.14413, 110.24301
21given(0.758083, 0.28893, 0.584662), (0.357575, -0.933882, -0.00213), (0.54539, 0.210676, -0.811274)-38.79326, -75.6298, 147.0369
22given(0.881949, 0.267817, -0.387866), (0.270136, -0.96154, -0.049682), (-0.386254, -0.060959, -0.920376)23.88871, -77.59416, 105.80286
23given(0.101986, 0.098044, -0.989942), (0.090764, -0.991898, -0.088887), (-0.990637, -0.080785, -0.110058)22.56467, -83.26202, 30.89696
24given(-0.808769, 0.015409, -0.587924), (-0.010698, -0.999877, -0.01149), (-0.588029, -0.003003, 0.808834)-42.74069, -93.26448, -5.02406
25given(1), (1), (1)
26given(0.523312, -0.053484, 0.850461), (-0.160754, 0.973912, 0.160164), (-0.836841, -0.220531, 0.501062)-83.54804, -18.95009, -17.89763
27given(-0.465676, -0.215875, 0.858222), (-0.311685, 0.947659, 0.06925), (-0.82825, -0.235247, -0.508587)-138.64627, -20.2962, 51.90207
28given(-0.97043, -0.241153, -0.010561), (-0.240385, 0.969464, -0.04852), (0.02194, -0.044546, -0.998766)-102.27466, -7.04921, 136.4299
29given(-0.471153, -0.232787, -0.850779), (-0.146153, 0.971816, -0.184967), (0.869859, 0.037196, -0.491897)-21.75395, 4.24316, 143.56549
30given(0.512415, -0.150193, -0.845502), (0.037724, 0.987573, -0.152568), (0.857909, 0.046282, 0.511712)26.66148, 10.46104, 74.62125
31given(-0.916757, -0.034015, 0.397994), (0.067617, -0.995203, 0.070696), (0.39368, 0.091722, 0.91466)-108.55981, -94.97082, 33.18823
32given(-0.130046, 0.081024, 0.988192), (0.258532, -0.959408, 0.112687), (0.957209, 0.270133, 0.10382)-107.35251, -87.61891, 110.87753
33given(0.746291, 0.320658, 0.583291), (0.392328, -0.919818, 0.003696), (0.537706, 0.226083, -0.812255)-38.4814, -74.70379, 146.98178
34given(0.878334, 0.256913, -0.403145), (0.269248, -0.962695, -0.026887), (-0.395013, -0.084931, -0.914741)24.61031, -79.12782, 104.92518
35given(0.09921, 0.12488, -0.987199), (0.075931, -0.990151, -0.117622), (-0.992165, -0.06329, -0.107715)22.90652, -82.37713, 31.02101
36given(-0.808223, 0.059673, -0.585845), (-0.045443, -0.998206, -0.038984), (-0.58712, -0.004885, 0.809485)-41.86206, -94.25135, -5.14019

-
Components

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


Mass: 54581.312 Da / Num. of mol.: 12 / Fragment: UNP residues 1-481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCP / Production host: Escherichia coli (E. coli) / References: UniProt: P55072, vesicle-fusing ATPase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M sodium citrate, pH 6.0, 0.3 M NaCl, 15.2 % PEG3350, 20 % glycerol, 2 % benzamidine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Mar 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.71→50 Å / Num. obs: 62997 / % possible obs: 88.8 % / Redundancy: 4.9 % / Net I/σ(I): 7.12

-
Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 3.71→50 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.833 / SU B: 172.044 / SU ML: 0.957 / Cross valid method: THROUGHOUT / ESU R Free: 1.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28527 2448 5.1 %RANDOM
Rwork0.24855 ---
obs0.25037 45977 68.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 140.215 Å2
Baniso -1Baniso -2Baniso -3
1--3.59 Å20 Å20 Å2
2--2.14 Å20 Å2
3---1.45 Å2
Refinement stepCycle: 1 / Resolution: 3.71→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41255 0 324 0 41579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01942240
X-RAY DIFFRACTIONr_bond_other_d0.0030.0241575
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.99357118
X-RAY DIFFRACTIONr_angle_other_deg1.173395756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.92155253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87124.1521970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.582157736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7715396
X-RAY DIFFRACTIONr_chiral_restr0.0810.26513
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02147188
X-RAY DIFFRACTIONr_gen_planes_other0.0030.028964
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_it2.2987.22621048
X-RAY DIFFRACTIONr_mcbond_other2.2987.22621047
X-RAY DIFFRACTIONr_mcangle_it4.12810.83626289
X-RAY DIFFRACTIONr_mcangle_other4.12810.83626290
X-RAY DIFFRACTIONr_scbond_it1.837.41121192
X-RAY DIFFRACTIONr_scbond_other1.837.41121193
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.44511.04430830
X-RAY DIFFRACTIONr_long_range_B_refined9.93967.801170732
X-RAY DIFFRACTIONr_long_range_B_other9.93967.801170733
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A27958.1
11B279510.31
11C279510.4
11D27959.18
11E279510.44
11F279510.77
11G27958.83
11H279510.48
11I27957.42
11J27958.79
11K279517.58
11L279513.72
22A26377.21
22B26376.28
22C26378.31
22D26378.39
22E263716.81
22F263710.71
22G26377.68
22H26378.6
22I26379.09
22J26377.96
22K26376.83
22L26378.6
33A13309.82
33B13308.99
33C133011.16
33D133010.39
33E13308.38
33F13309.21
33G13307.04
33H13307.76
33I13308.32
33J13309.73
33K13308.95
33L133010.24
LS refinement shellResolution: 3.71→3.805 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.57 33 -
Rwork0.463 681 -
obs--13.78 %
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)
14.54591.55513.8315.22091.49517.95870.06420.30130.2014-0.2989-0.1075-0.5431-0.29390.20210.04330.3133-0.11470.33740.24340.13760.80399.4683-58.846436.183
27.1485-3.3193-4.42827.35343.192410.4379-0.0634-0.07340.93640.1090.0456-0.1848-0.40960.77610.01780.1754-0.075-0.28340.5437-0.11150.67829.8619-55.442699.3618
36.935-0.4382-1.18324.79822.06853.40280.0184-1.09830.16530.44830.01520.1326-0.174-0.0931-0.03371.26860.03850.05941.1045-0.22090.5673-43.6788-64.1677132.136
45.5096-1.18052.95776.1177-3.25769.3983-0.2902-0.2440.08090.59160.35450.06840.0013-0.3986-0.06430.22480.07950.23440.7068-0.34840.6828-98.0126-71.8353101.5424
55.80641.557-3.75045.033-2.49586.87420.5287-0.43181.2921-0.3334-0.12191.0483-0.3473-0.7907-0.40670.8845-0.0024-0.39140.6788-0.19121.1625-99.157-72.45938.1499
69.22571.15970.56983.46551.09822.95840.10590.5426-0.017-0.5665-0.10.0175-0.27990.1058-0.00591.2261-0.0741-0.08890.48280.3020.3764-44.6793-67.65085.5035
75.2921.44190.25314.6565-2.02099.028-0.19630.3981-0.4915-0.25510.10880.41740.113-0.57790.08760.7448-0.14840.07720.3578-0.20861.0655-104.3289-40.038851.8029
87.6939-2.59283.02295.4235-1.26274.85780.0809-0.6144-0.92240.4606-0.18530.58820.6414-0.8470.10441.5446-0.18820.38170.62310.12460.5656-79.6733-37.9759110.4684
99.2167-0.7608-1.43846.46611.39595.5989-0.2654-0.8413-0.45950.4621-0.1076-0.05570.26640.25970.3731.02480.0369-0.50450.55680.04840.3192-17.7773-24.7605117.9484
103.0368-1.1919-0.55855.76961.34935.6974-0.0972-0.8295-0.29150.19220.3165-0.89620.46360.8971-0.21930.79870.1374-0.17910.9486-0.04071.178319.429-17.747668.719
118.8104-0.24841.42537.31810.25893.33530.09920.37740.13590.0751-0.2025-0.8763-0.21030.12030.10330.6165-0.06760.22690.4311-0.0680.2229-4.4067-25.167510.2011
127.2813.46-2.04847.9202-1.05815.7431-0.37170.06840.3306-0.21840.0629-0.08140.05760.19640.30880.60110.1949-0.30440.4814-0.15070.2069-66.749-33.09712.0351
136.7978-1.46211.92412.3410.11475.962-0.08770.05620.28430.06050.0718-0.01670.1164-0.2590.01590.2061-0.0370.14820.09080.08350.2781-13.811-67.180151.1632
143.4741-0.0150.98933.7005-1.60418.1-0.2046-0.17470.16390.02470.1427-0.0925-0.0227-0.02810.06190.04150.0786-0.10050.2515-0.11780.4175-13.3847-65.984585.8089
156.2132.0536-1.77324.2961-1.39426.82890.1303-0.29140.03620.1741-0.06880.1828-0.018-0.2439-0.06150.30510.1961-0.12560.5578-0.11520.2498-42.7691-71.1589104.0898
168.34542.49791.44783.50960.9793.5848-0.21090.0311-0.0324-0.2555-0.0363-0.00760.2991-0.09190.24710.23760.02240.22730.449-0.14450.3879-73.1113-75.785987.0306
174.4541-0.0851-1.67792.81581.84556.9172-0.0114-1.13210.8377-0.09850.104-0.1458-0.1563-0.0788-0.09260.4612-0.2089-0.17430.7748-0.11720.7166-73.7402-75.024452.2141
187.666-0.19280.09162.21821.54075.956-0.02-0.66640.2251-0.1043-0.1231-0.02450.0995-0.59070.14310.6717-0.0833-0.16080.2050.11330.2549-44.0106-71.725134.0817
196.129-0.922-1.62282.86350.9666.24070.01550.27940.20430.06950.06590.247-0.1272-0.0837-0.08150.50710.0604-0.06260.1944-0.15620.2146-77.7655-29.261656.0372
204.70840.58860.61853.34541.66626.4923-0.25180.1957-0.03480.22710.0186-0.07470.2853-0.26920.23320.71190.04650.13780.1657-0.07430.0793-64.2601-28.050488.307
216.52061.81390.40854.13510.20044.7819-0.1981-0.11250.1781-0.190.0515-0.0553-0.06810.08040.14660.92410.1012-0.26740.2215-0.05670.0913-30.4574-20.597392.3403
223.95342.3585-1.85063.5486-1.17236.65850.2389-0.4072-0.01550.11620.0157-0.10480.21950.2841-0.25460.5459-0.0057-0.20950.3576-0.15970.3648-9.4079-16.905264.2056
236.1167-0.00190.71542.9072-0.7766.11440.093-0.28430.04120.09310.05770.1097-0.41620.0138-0.15070.5269-0.0750.10790.1348-0.09680.0872-22.3248-20.856532.4127
247.2137-0.70140.0052.6782-0.75634.52130.04860.0325-0.03140.2619-0.00030.1518-0.27550.2095-0.04830.68390.0879-0.09880.182-0.07130.0472-56.6574-25.517328.1277
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 200
2X-RAY DIFFRACTION2B21 - 200
3X-RAY DIFFRACTION3C21 - 200
4X-RAY DIFFRACTION4D21 - 200
5X-RAY DIFFRACTION5E21 - 200
6X-RAY DIFFRACTION6F21 - 200
7X-RAY DIFFRACTION7G21 - 200
8X-RAY DIFFRACTION8H21 - 200
9X-RAY DIFFRACTION9I21 - 200
10X-RAY DIFFRACTION10J21 - 200
11X-RAY DIFFRACTION11K21 - 200
12X-RAY DIFFRACTION12L21 - 200
13X-RAY DIFFRACTION13A201 - 460
14X-RAY DIFFRACTION13A800
15X-RAY DIFFRACTION14B201 - 458
16X-RAY DIFFRACTION14B800
17X-RAY DIFFRACTION15C201 - 458
18X-RAY DIFFRACTION15C800
19X-RAY DIFFRACTION16D201 - 459
20X-RAY DIFFRACTION16D800
21X-RAY DIFFRACTION17E201 - 458
22X-RAY DIFFRACTION17E800
23X-RAY DIFFRACTION18F201 - 458
24X-RAY DIFFRACTION18F800
25X-RAY DIFFRACTION19G201 - 458
26X-RAY DIFFRACTION19G800
27X-RAY DIFFRACTION20H201 - 459
28X-RAY DIFFRACTION20H800
29X-RAY DIFFRACTION21I201 - 459
30X-RAY DIFFRACTION21I800
31X-RAY DIFFRACTION22J201 - 461
32X-RAY DIFFRACTION22J800
33X-RAY DIFFRACTION23K201 - 459
34X-RAY DIFFRACTION23K800
35X-RAY DIFFRACTION24L201 - 458
36X-RAY DIFFRACTION24L800

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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