[English] 日本語
Yorodumi
- PDB-8afi: GABARAP in complex with LIR motif of HsATG3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8afi
TitleGABARAP in complex with LIR motif of HsATG3
Components
  • Gamma-aminobutyric acid receptor-associated protein
  • Ubiquitin-like-conjugating enzyme ATG3
KeywordsSIGNALING PROTEIN / Autophagy / LIR / ATG3 / GABARAP
Function / homology
Function and homology information


Atg12 transferase activity / Atg8-family conjugating enzyme activity / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / ubiquitin-like protein transferase activity / positive regulation of protein K48-linked ubiquitination / regulation of cilium assembly / glycophagy / regulation of Rac protein signal transduction / nucleophagy ...Atg12 transferase activity / Atg8-family conjugating enzyme activity / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / ubiquitin-like protein transferase activity / positive regulation of protein K48-linked ubiquitination / regulation of cilium assembly / glycophagy / regulation of Rac protein signal transduction / nucleophagy / mitochondrial fragmentation involved in apoptotic process / GABA receptor binding / autophagy of mitochondrion / phosphatidylethanolamine binding / phagophore assembly site / Transferases; Acyltransferases; Aminoacyltransferases / TBC/RABGAPs / cellular response to nitrogen starvation / protein targeting to membrane / microtubule associated complex / negative regulation of phagocytosis / Macroautophagy / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / smooth endoplasmic reticulum / autophagosome membrane / axoneme / extrinsic apoptotic signaling pathway via death domain receptors / autophagosome assembly / autophagosome maturation / protein targeting / beta-tubulin binding / mitophagy / sperm midpiece / autophagosome / GABA-ergic synapse / microtubule cytoskeleton organization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / lysosome / protein ubiquitination / Golgi membrane / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / enzyme binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Ubiquitin-like-conjugating enzyme ATG3 / Gamma-aminobutyric acid receptor-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsFarnung, J. / Benoit, R.M. / Corn, J.E. / Bode, J.W.
Funding support Switzerland, European Union, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation188634 Switzerland
Swiss National Science Foundation310030_201160 Switzerland
European Research Council (ERC)856581European Union
CitationJournal: Acs Cent.Sci. / Year: 2023
Title: Semisynthetic LC3 Probes for Autophagy Pathways Reveal a Noncanonical LC3 Interacting Region Motif Crucial for the Enzymatic Activity of Human ATG3.
Authors: Farnung, J. / Muhar, M. / Liang, J.R. / Tolmachova, K.A. / Benoit, R.M. / Corn, J.E. / Bode, J.W.
History
DepositionJul 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein
C: Gamma-aminobutyric acid receptor-associated protein
F: Ubiquitin-like-conjugating enzyme ATG3
H: Ubiquitin-like-conjugating enzyme ATG3
B: Ubiquitin-like-conjugating enzyme ATG3
J: Ubiquitin-like-conjugating enzyme ATG3
N: Ubiquitin-like-conjugating enzyme ATG3
P: Ubiquitin-like-conjugating enzyme ATG3
D: Ubiquitin-like-conjugating enzyme ATG3
L: Ubiquitin-like-conjugating enzyme ATG3
E: Gamma-aminobutyric acid receptor-associated protein
G: Gamma-aminobutyric acid receptor-associated protein
I: Gamma-aminobutyric acid receptor-associated protein
K: Gamma-aminobutyric acid receptor-associated protein
M: Gamma-aminobutyric acid receptor-associated protein
O: Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,83825
Polymers131,07516
Non-polymers7639
Water39622
1
A: Gamma-aminobutyric acid receptor-associated protein
B: Ubiquitin-like-conjugating enzyme ATG3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5364
Polymers16,3842
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-2 kcal/mol
Surface area7350 Å2
MethodPISA
2
C: Gamma-aminobutyric acid receptor-associated protein
D: Ubiquitin-like-conjugating enzyme ATG3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5364
Polymers16,3842
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-2 kcal/mol
Surface area7300 Å2
MethodPISA
3
F: Ubiquitin-like-conjugating enzyme ATG3
E: Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4763
Polymers16,3842
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-3 kcal/mol
Surface area7340 Å2
MethodPISA
4
H: Ubiquitin-like-conjugating enzyme ATG3
G: Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4763
Polymers16,3842
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-3 kcal/mol
Surface area7140 Å2
MethodPISA
5
J: Ubiquitin-like-conjugating enzyme ATG3
I: Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4763
Polymers16,3842
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-5 kcal/mol
Surface area7390 Å2
MethodPISA
6
N: Ubiquitin-like-conjugating enzyme ATG3
M: Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4763
Polymers16,3842
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-3 kcal/mol
Surface area7040 Å2
MethodPISA
7
P: Ubiquitin-like-conjugating enzyme ATG3
O: Gamma-aminobutyric acid receptor-associated protein


Theoretical massNumber of molelcules
Total (without water)16,3842
Polymers16,3842
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-6 kcal/mol
Surface area7270 Å2
MethodPISA
8
L: Ubiquitin-like-conjugating enzyme ATG3
K: Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4763
Polymers16,3842
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-5 kcal/mol
Surface area7080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.800, 63.800, 73.900
Angle α, β, γ (deg.)64.500, 86.500, 70.300
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
12
22
32
42
52
13
23
33

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEPHETYRTYR(chain 'A' and (resid 3 through 12 or (resid 13...AA3 - 1152 - 114
221PHEPHETYRTYR(chain 'C' and (resid 3 through 12 or (resid 13...CB3 - 1152 - 114
331PHEPHETYRTYR(chain 'E' and (resid 3 through 12 or (resid 13...EK3 - 1152 - 114
441PHEPHETYRTYR(chain 'G' and (resid 3 through 12 or (resid 13...GL3 - 1152 - 114
551PHEPHETYRTYR(chain 'I' and (resid 3 through 12 or (resid 13...IM3 - 1152 - 114
661PHEPHETYRTYR(chain 'K' and (resid 3 through 12 or (resid 13...KN3 - 1152 - 114
771PHEPHETYRTYR(chain 'M' and (resid 3 through 22 or (resid 23...MO3 - 1152 - 114
881PHEPHETYRTYR(chain 'O' and (resid 3 through 12 or (resid 13...OP3 - 1152 - 114
192ALAALATHRTHR(chain 'B' and resid 96 through 110)BE96 - 1107 - 21
2102ALAALATHRTHR(chain 'D' and resid 96 through 110)DI96 - 1107 - 21
3112ALAALATHRTHR(chain 'F' and resid 96 through 110)FC96 - 1107 - 21
4122ALAALATHRTHR(chain 'J' and resid 96 through 110)JF96 - 1107 - 21
5132ALAALATHRTHRchain 'L'LJ96 - 1107 - 21
1143ASPASPTHRTHR(chain 'H' and resid 104 through 110)HD104 - 11015 - 21
2153ASPASPTHRTHR(chain 'N' and resid 104 through 110)NG104 - 11015 - 21
3163ASPASPTHRTHRchain 'P'PH104 - 11015 - 21

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
Gamma-aminobutyric acid receptor-associated protein / GABA(A) receptor-associated protein / MM46


Mass: 13697.693 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAP, FLC3B, HT004 / Plasmid: pOPINS / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-CodonPlus (DE3) RIL / References: UniProt: O95166
#2: Protein/peptide
Ubiquitin-like-conjugating enzyme ATG3


Mass: 2686.685 Da / Num. of mol.: 8 / Mutation: N113G / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: C9JNW8
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Sodium acetate, sodium cacodylate, PEG 8,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.66→49.13 Å / Num. obs: 52724 / % possible obs: 98.14 % / Redundancy: 3.5 % / Biso Wilson estimate: 72.38 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.06833 / Rpim(I) all: 0.04274 / Rrim(I) all: 0.0809 / Net I/σ(I): 14.19
Reflection shellResolution: 2.66→2.75 Å / Rmerge(I) obs: 1.126 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 2663 / CC1/2: 0.481 / CC star: 0.806 / Rpim(I) all: 0.7205

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDS1.16_3549data reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HB9

6hb9


Resolution: 2.66→49.1 Å / SU ML: 0.4485 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 30.8705
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2618 2637 5 %
Rwork0.2146 50087 -
obs0.217 52724 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.52 Å2
Refinement stepCycle: LAST / Resolution: 2.66→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8485 0 50 22 8557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01158751
X-RAY DIFFRACTIONf_angle_d1.216511787
X-RAY DIFFRACTIONf_chiral_restr0.0681204
X-RAY DIFFRACTIONf_plane_restr0.00891527
X-RAY DIFFRACTIONf_dihedral_angle_d11.38985204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.710.38461320.38462434X-RAY DIFFRACTION88.48
2.71-2.760.39591400.36712687X-RAY DIFFRACTION95.57
2.76-2.820.40441350.3622628X-RAY DIFFRACTION95.67
2.82-2.880.35241400.33542673X-RAY DIFFRACTION95.75
2.88-2.940.33391460.31672718X-RAY DIFFRACTION95.59
2.94-3.020.3191390.30812608X-RAY DIFFRACTION95.38
3.02-3.10.31911390.2832654X-RAY DIFFRACTION95.98
3.1-3.190.34191430.25932736X-RAY DIFFRACTION95.78
3.19-3.290.2891360.25882609X-RAY DIFFRACTION95.18
3.29-3.410.2891410.24132682X-RAY DIFFRACTION95.44
3.41-3.550.27481420.23962682X-RAY DIFFRACTION95.15
3.55-3.710.2471390.22832685X-RAY DIFFRACTION95.66
3.71-3.90.25781400.21112594X-RAY DIFFRACTION93.82
3.9-4.150.24711400.19592613X-RAY DIFFRACTION94.22
4.15-4.470.22231360.17112602X-RAY DIFFRACTION93.96
4.47-4.920.18961350.15312638X-RAY DIFFRACTION92.62
4.92-5.630.28471380.19512548X-RAY DIFFRACTION93.07
5.63-7.090.24331400.19932692X-RAY DIFFRACTION95.61
7.09-49.10.23291360.17622604X-RAY DIFFRACTION93.84
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)
19.085887801061.20029248541-3.143693489227.28417443575-1.614611162874.85038312819-0.1000851420680.1187576066690.445677730893-1.56554684062-0.124211257254-0.4315391850430.2896113468130.1879206970610.01895234495551.040815438220.02100741055640.06084230941730.995312016834-0.1133091568360.56435595958928.41912389410.0163963286348-46.5281315087
25.646487377440.7248626261280.9392634393887.769709706690.7154181800919.284065164480.171237432998-0.251860300195-0.3943990427770.0340366884708-0.0492153067417-0.2254975717771.10443447838-0.207234124073-0.1645207444030.328783954611-0.005213965728850.033861763120.5429601311330.03195559469480.41098884637526.31823643331.34894016452-30.5008743772
35.86955293446.356348335515.650177813137.635467758596.26216419315.48365777042-1.58989691519-1.046189576831.33874135858-2.25601949241.39255628512.55734653353-1.97215633747-1.594803523690.6279743960921.08526107372-0.0669479012364-0.2563312689091.641416925150.157276656110.78772342485824.352574691121.9304961619-48.5403616006
47.93008090541-0.857066966730.1408695240456.789493617732.899420375075.27827501811-0.313830131861.94673054251.0820995704-1.849871158070.455222638842-0.3128890412720.7354545289820.2293637930260.03475011302751.12823881801-0.07611821293360.2112785387891.340970374590.02740400640170.60391652051434.115808423815.3198476861-55.0246477461
52.977310844272.084686342943.378708153669.276126618121.810515894796.49234343765-0.3521401421311.5401484152-1.48418731728-0.5199425488330.0751131923846-0.454692754892-0.08766849531131.14300836995-0.2400345064430.676077977585-0.1007002539660.03183628762851.067077814270.1343796750460.53967791461938.979963847123.1227336119-47.8481703732
63.223722043932.82797637568-3.715049505859.26853880743-6.048708264546.695430170321.117560159861.074342354432.06269488227-0.4100098734131.269153929390.5241285038111.3889614019-0.161009799687-1.662297798521.158920421550.101424934507-0.06593647882261.50939214158-0.001651845469381.1969358535728.260427787233.141801898-40.6754141104
77.884292116141.748289338094.383322162229.192096184373.629123027664.956847082970.2633029264750.2383839445450.227223535593-0.486706900071-0.033911451801-1.63726655584-0.8076001022891.102386183150.07832944059210.757718827196-0.269481677960.1159461404671.263488366720.1875043420010.82913898711742.219895394229.683121139-41.5878733002
85.520833314880.1190156236682.583036264866.915949673822.917839771447.572036682770.02507636097010.2287300328880.1783989337570.734946664801-0.277236645706-0.4877584535180.2348468007110.3141068575020.1944360095320.678843856506-0.02297343123180.06493323968110.6574601171670.1603152044280.52053499618935.668044923223.6405765295-36.8237849353
91.76096933763-0.0738685835653-0.1379647969441.743611844841.28321386158.401119843663.33597391221.01611508781-0.811893439904-1.93513294198-0.8918152509550.0147058797329-1.68529620567-0.589227766482-1.91696157831.748673468120.067771050157-0.1911293283561.48525347070.1479151011831.43790316771-1.1228719964523.2392549309-40.6944727936
107.35317959685-0.815235336956-2.183431539444.886347582894.886022339135.157144021091.08530387571-0.440705991334-0.2506920440171.611559971840.669498202604-0.559086758173-1.32529300341.68994943144-1.566503785981.45244535961-0.09241773343140.07418693405640.8375643934850.1057436120361.1333947342.771942404719.9392386267-32.0762961293
117.78670145166-3.99713523239-2.598003865525.958094044720.865157434336.86605717005-0.6428695970840.194745007464-0.561662898250.4249938385430.9649299314490.634474903749-0.479568517748-0.386049726278-0.0267358858020.9933881621350.1087813238460.2975552193981.225732891950.1126329931631.1451838991423.97460728117.05266664846.23632988199
124.414372560791.697396925062.191073354313.81819334857-0.4335770160821.56794037811-0.1894150717470.89174720725-1.41999815248-1.16292788316-1.73135877336-0.8253712230980.782395846841-0.7300918042521.439345541611.935556681020.1854417124870.1213055875910.963189739891-0.1413959083881.3984505400926.0069518921-13.3847368079-41.7072260402
139.49543133284-1.82099957838-9.10121594124.492835618482.692881914628.96602822593-3.348177695731.083435180990.00738250850672-0.5301032390890.0751558549338-0.3700836042570.377285073559-1.814975609891.216596409891.17150538152-0.220417825435-0.3198127027190.956208235470.1830510914110.95454734106923.3538444805-9.49077921707-37.5357681597
148.074898117470.1991438009980.9050839186125.41657000374-4.349973183634.495514596290.604659511326-0.331691621264-1.282523541542.23307462684-0.728624154053-1.745811107242.62033618376-0.542168948184-1.097788806192.11170805523-0.3604487302740.03638003146231.75447514688-0.4679888983791.10897362709-6.164665425316.1159538555715.6423045914
155.538405218691.48120218837-2.627191832262.251173026970.5727225502932.10840494226-0.0904737271769-1.47671553092-0.5897406507882.39478905056-0.423878619168-0.3237907161740.107265638737-2.06312789028-0.006310416938491.00236139674-0.282690873351-0.5899958063322.17428154464-0.405004094458-0.0498182003642-6.688829106475.199804653710.0268713245
166.181685446762.903907354222.72751416124.99324781811-1.200773343942.938115238740.237102920892-0.636548683097-1.05349260632-1.09787458774-0.9372637555930.392272182963-0.116461525502-1.164941520440.1589650578081.80948524888-0.1843296768770.09962247239172.17212137323-0.4577571169440.85225342190111.677511831440.684403077-49.3864782457
175.147425131423.02254268064-4.162116136383.31686903349-1.584830340044.31712080733-0.776220943783-0.223202675119-0.912239727985-0.0609561070364-0.891658721989-0.2882316913591.14175933717-0.5625805284422.01725185041.54553646069-0.2334263454560.2009215488551.52211575067-0.1464819569721.2687295740142.269078072742.88080638-7.11701400113
186.515211710942.66780013832-5.296659146654.30436639437-0.195852796326.61740038099-0.2118434902230.6702627457461.00346941906-1.598465676520.9567051377642.04395351014-0.443280385796-0.1607198487490.3088355099141.69717601174-0.3140309540050.1812686211041.754704835310.3728636348750.99133890008337.091233803629.8448181189-56.4837201308
197.027688187591.307857977994.664023527927.260203629051.641006358633.17450556062-0.7315378131111.07710601265-0.739539057372-1.455953645591.04799450779-1.459685921540.3933152838241.823020028522.005243552551.05763835369-0.2521499676280.07532285178651.433691287450.1326076583410.96552978835942.955794803929.5515351381-50.6513496771
202.569873768580.741654466280.4071303018881.87298127318-1.24688126541.226719172190.426234356719-0.7293661224451.646379534481.335338879550.4132617336121.098022685160.7381635031490.0801089166141-1.539044252961.32858400874-0.1570731639170.1550890633961.497034725260.1779814711531.576475255-2.3914675872128.3566746435-2.49613118347
214.552098976891.90040927898-0.5347309499787.79666069375-0.7960260747926.1628288386-0.3778407029571.195188547030.212919510857-1.564549577350.3680291860460.2253550177590.0369109979152-0.3562524029060.1080108308490.879058312780.0316252531705-0.1105557065050.9367308458130.151844176690.615939705696-0.46343805252810.8752576616-40.8478058866
225.46237905401-0.0827091572035-4.603953912817.64346782022-1.073899559414.74896904079-0.08288369955810.9783776232891.09371799503-0.4373431257110.3022465922110.749670934246-0.709272147192-0.628305742906-0.09214415361620.635069465633-0.0182599253264-0.07277347190640.737378486012-0.04567865188120.676161385714-3.778522721713.7863755352-25.8420026451
238.107334048221.00766556193-1.582308706837.11145971095-1.204139207856.6611011034-0.2860817373650.387759405236-0.04754050729-0.083747073291-0.03549847656640.390768936203-0.196114187751-0.4257143290920.2510276952060.318197541276-0.04259394191-0.07775376560320.551307807483-0.05366021683610.440486849523-2.771480509155.79793584784-26.7674892696
243.970003227910.585054996174-2.145337959558.843535694751.534689645656.67891336389-0.161861058607-0.9378706910530.1120083954791.697071544090.1959578717840.584184664771-1.69721057269-0.6611555126060.05765516460321.092376093780.1605508237340.1687900327651.39879970473-0.03067921638170.51025371617326.763894634317.03563136894.95300464631
253.789603549652.072060848192.021221284215.458982113661.728382097481.1666366486-0.309216249414-1.47378494107-1.334021428840.999491765276-0.3688296017281.85600915349-0.141284775281-2.148332390730.3651545852520.7298187826260.146200768830.01075271582492.22886032761-0.09810166288031.0413448144215.274567346310.1680534818-7.20225448413
267.38661135435-0.2813602385990.01055489546177.48409794240.7258939028035.75445581363-0.06603638101060.0301677179766-0.5141055872530.348503968517-0.08522347474350.0892720971231-0.217377958-0.177842952360.2758929302110.5199558880410.01987193462250.05537788108840.9963404456290.008628372213450.34399171343827.69105552348.9290789451-7.50753490677
271.884115603882.784126398822.187840720745.77557004260.7209126328286.79013120540.604697719384-1.54436121356-0.5440959059440.804931442033-0.939638958236-0.2711371740951.576337742820.7135608664720.3931835826361.134959522060.174682184164-0.0624411378141.645983116940.2357236458550.570585550474-7.94235876983-7.115874348569.33912015771
281.27005460581.248094690461.615118887865.89912405347-2.569754257386.262008834920.0551291310242-1.492009172470.6043506281010.56687565673-0.200188885311-0.767876401462-0.66639041961.7314440281-0.1361318812110.776531108018-0.0429742805131-0.1860950638791.24908408165-0.07857253581020.513394609922-3.020960507072.319648714511.0845407423
297.03923139865-0.819106832614-1.553620272076.636492126870.07141050183483.219078722960.721607782769-1.092539585691.097871834061.00704423161-0.3070326441960.093403579815-0.9313868470070.355337729782-0.2325317540910.6656540638-0.08718985674890.050879101370.969138122483-0.1879559766290.552517092699-8.679200033699.21252109858-1.4247728136
306.31681353932-1.64410671882-0.2147195251196.83589710745-0.7682188788558.907439196310.137807096345-0.3608876724030.2293626051390.395909787859-0.106546858071-0.1212994525590.04198920321080.227001219188-0.1424803620930.477194217811-0.0271787101207-0.09947788032050.865826525203-0.06659613183340.335557597944-7.041926588430.617036155055-6.18806279422
314.865752185322.817161748042.525685925769.82284599154-3.50094791554.55749716482-1.31753896703-1.006934897491.114638417290.6452485958671.344190440591.301789108260.162920427708-2.260041899970.6514639617710.9406408233820.06127521053510.3776278476481.480730497290.003021289178631.15580802943-1.1544411212244.5986910662-0.664568911159
325.133916102680.1010192114832.534073784335.18886681254-1.757842790458.372545869850.211077948975-1.28250118263-1.272928798211.048269521250.3830338820790.6526924937240.539175930833-0.685682751255-0.1675376488560.806776344998-0.01602925962490.2065847977010.9901179687760.221763207170.9218974829134.05735794834.8616637579-4.3349513557
331.059066891970.08743202567961.275615809588.03953775843-1.432244197051.870046540850.7176067428040.851194294902-1.87588945788-0.957781837571-0.626620716287-0.7491675629181.52897750542-1.35821032265-0.2326238989431.19863317732-0.172750254950.3072918549411.00781208921-0.2351503597481.173293965754.3903934369632.7892725285-18.8356636734
348.84510002791-0.717338658969-1.935449832317.29612396934-2.618449849366.47072012304-0.4439524150810.119607904552-0.5997163610910.376133071720.189734560136-0.1028940499410.4713552915060.3267067564750.06645282251310.6624642814570.08059642681780.161346626510.764285149338-0.04948357559980.6992631502498.3390311689441.0375993641-13.1668266697
351.531411744451.29960418107-3.505005690124.00814376623-3.960375706678.52232880984-0.411275690866-1.14173783272-0.308474236403-1.43758065127-0.084040041346-2.088936661261.555982760771.066605709330.6051966589410.889755994396-0.2561157238390.1277426479831.49340920931-0.04903639428831.0064956258324.99152473148.4158034747-43.9270879537
361.56733091322-1.520330364151.819118252025.01440016096-0.4729872311073.602239734130.7436350732871.64991412666-0.505290028286-1.55583451881-0.3297880238640.00980425618092-2.14532834235-0.3204820453120.2634564835771.2572019645-0.25190582354-0.07137260639171.72074138968-0.1821151910340.67380666180215.852240855354.2820426606-52.3499265722
373.872153091083.56404588038-1.578639029686.456536841091.306556804013.05871465538-0.9101436222422.179718013321.16994709392-0.580701203899-0.1209215951020.9076748171990.0356003752659-0.7420031909220.08955632390660.736941411075-0.280490229130.08136749411161.62351657244-0.336831340140.59328775067510.579717644746.4021389765-45.7664233076
387.22430508462-1.837263731452.622676911177.01066054816-1.213623030817.90759987507-0.3411198169120.617206773323-1.05255681386-0.6940614320930.2657473163290.06768944210840.3894164494820.9783187212380.2507919357930.717736867745-0.154743008246-0.002917925115651.21959393913-0.2630692098190.82727829674413.704128233440.5634869817-39.6464915669
399.00223132407-3.587479456281.895023258726.13873997789-1.605897627184.90585302453-0.175319217775-1.18175178239-1.509435094230.0981058631020.2313121397471.561735441941.35123158719-1.07074531872-0.1079954322430.884408032414-0.468880054020.2210698749871.14038401083-0.4163776328541.064119943726.0325220540437.798831967-36.5340476883
409.23275088720.871873704272-2.176552317335.7576458606-1.909522645727.42397740688-0.6292668060040.176189835243-1.18281417310.19952895230.2551135489040.3896469652080.594302485650.09345865300690.3117536832780.528192728605-0.111868582070.1808543453290.66153125407-0.2101915167760.6747262657839.9375781616941.5128749729-30.6580013325
416.381072391612.4538735361-1.913438057327.05130250382-4.552074461925.33082591778-0.123651120630.902246684485-0.1213546185370.04937474490560.0280066057450.283221302586-0.435337249424-0.4729074873610.004579100603680.802876169806-0.1697038721650.06846376189731.07054571253-0.3397662584050.5922077367613.002466322650.5707425506-37.4668548153
422.133669105651.24897045903-1.592721471511.26262691529-1.071055187627.84343303341-0.0350784298964-0.255478497388-0.04175555775872.313640106980.0206666665508-0.4796733316420.139234880869-0.372081398602-0.01510096167881.74859773076-0.049064642068-0.3542572944381.29513541281-0.1384968053720.91035648928136.829749470435.8530987602-1.98127451162
438.85145909486-0.458286024723-0.8840265296219.003548418592.533581851059.93334555130.263087737079-0.483367850470.6206794035610.3734635344440.172803380974-0.391100614306-0.93660581280.404012317016-0.3592204844911.340591439070.0123523534414-0.1100498595240.8045025603120.001559242777340.55698418239937.841315918532.7627194581-16.3894167969
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 116 )
3X-RAY DIFFRACTION3chain 'C' and (resid 3 through 10 )
4X-RAY DIFFRACTION4chain 'C' and (resid 11 through 24 )
5X-RAY DIFFRACTION5chain 'C' and (resid 25 through 35 )
6X-RAY DIFFRACTION6chain 'C' and (resid 36 through 47 )
7X-RAY DIFFRACTION7chain 'C' and (resid 48 through 68 )
8X-RAY DIFFRACTION8chain 'C' and (resid 69 through 116 )
9X-RAY DIFFRACTION9chain 'F' and (resid 96 through 105 )
10X-RAY DIFFRACTION10chain 'F' and (resid 106 through 111 )
11X-RAY DIFFRACTION11chain 'H' and (resid 104 through 111 )
12X-RAY DIFFRACTION12chain 'B' and (resid 95 through 104 )
13X-RAY DIFFRACTION13chain 'B' and (resid 105 through 110 )
14X-RAY DIFFRACTION14chain 'J' and (resid 95 through 102 )
15X-RAY DIFFRACTION15chain 'J' and (resid 103 through 111 )
16X-RAY DIFFRACTION16chain 'N' and (resid 103 through 111 )
17X-RAY DIFFRACTION17chain 'P' and (resid 104 through 110 )
18X-RAY DIFFRACTION18chain 'D' and (resid 93 through 107 )
19X-RAY DIFFRACTION19chain 'D' and (resid 108 through 110 )
20X-RAY DIFFRACTION20chain 'L' and (resid 96 through 110 )
21X-RAY DIFFRACTION21chain 'E' and (resid 2 through 35 )
22X-RAY DIFFRACTION22chain 'E' and (resid 36 through 67 )
23X-RAY DIFFRACTION23chain 'E' and (resid 68 through 116 )
24X-RAY DIFFRACTION24chain 'G' and (resid 3 through 35 )
25X-RAY DIFFRACTION25chain 'G' and (resid 36 through 47 )
26X-RAY DIFFRACTION26chain 'G' and (resid 48 through 116 )
27X-RAY DIFFRACTION27chain 'I' and (resid 2 through 24 )
28X-RAY DIFFRACTION28chain 'I' and (resid 25 through 47 )
29X-RAY DIFFRACTION29chain 'I' and (resid 48 through 67 )
30X-RAY DIFFRACTION30chain 'I' and (resid 68 through 116 )
31X-RAY DIFFRACTION31chain 'K' and (resid 2 through 10 )
32X-RAY DIFFRACTION32chain 'K' and (resid 11 through 56 )
33X-RAY DIFFRACTION33chain 'K' and (resid 57 through 67 )
34X-RAY DIFFRACTION34chain 'K' and (resid 68 through 116 )
35X-RAY DIFFRACTION35chain 'M' and (resid 3 through 10 )
36X-RAY DIFFRACTION36chain 'M' and (resid 11 through 24 )
37X-RAY DIFFRACTION37chain 'M' and (resid 25 through 35 )
38X-RAY DIFFRACTION38chain 'M' and (resid 36 through 56 )
39X-RAY DIFFRACTION39chain 'M' and (resid 57 through 67 )
40X-RAY DIFFRACTION40chain 'M' and (resid 68 through 90 )
41X-RAY DIFFRACTION41chain 'M' and (resid 91 through 115 )
42X-RAY DIFFRACTION42chain 'O' and (resid 2 through 35 )
43X-RAY DIFFRACTION43chain 'O' and (resid 36 through 116 )

+
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