[English] 日本語
Yorodumi
- PDB-8t31: Crystal structure of GABARAP in complex with the LIR of TP53INP2/DOR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8t31
TitleCrystal structure of GABARAP in complex with the LIR of TP53INP2/DOR
Components
  • Gamma-aminobutyric acid receptor-associated protein
  • Tumor protein p53-inducible nuclear protein 2
KeywordsPROTEIN BINDING / Autophagy / GABARAP selectivity / DOR LIR / TP53INP2 LIR
Function / homology
Function and homology information


negative regulation of protein localization / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / tissue homeostasis / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane ...negative regulation of protein localization / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / tissue homeostasis / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Macroautophagy / beta-tubulin binding / autophagosome membrane / extrinsic apoptotic signaling pathway via death domain receptors / axoneme / autophagosome assembly / autophagosome maturation / smooth endoplasmic reticulum / protein targeting / mitophagy / sperm midpiece / autophagosome / ubiquitin binding / GABA-ergic synapse / PML body / microtubule cytoskeleton organization / osteoblast differentiation / intracellular protein localization / protein transport / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / ubiquitin-dependent protein catabolic process / microtubule binding / cytoplasmic vesicle / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / nucleus / plasma membrane / cytosol
Similarity search - Function
Tumour protein p53-inducible nuclear protein / DOR family / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein / Tumor protein p53-inducible nuclear protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.096 Å
AuthorsAli, M.G.H. / Wahba, H.M. / Cyr, N. / Omichinski, J.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Autophagy / Year: 2024
Title: Structural and functional characterization of the role of acetylation on the interactions of the human Atg8-family proteins with the autophagy receptor TP53INP2/DOR.
Authors: Ali, M.G. / Wahba, H.M. / Igelmann, S. / Cyr, N. / Ferbeyre, G. / Omichinski, J.G.
History
DepositionJun 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.2Sep 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 11, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein
B: Tumor protein p53-inducible nuclear protein 2
C: Gamma-aminobutyric acid receptor-associated protein
D: Tumor protein p53-inducible nuclear protein 2
E: Gamma-aminobutyric acid receptor-associated protein
F: Tumor protein p53-inducible nuclear protein 2
G: Gamma-aminobutyric acid receptor-associated protein
H: Tumor protein p53-inducible nuclear protein 2
I: Gamma-aminobutyric acid receptor-associated protein
J: Tumor protein p53-inducible nuclear protein 2


Theoretical massNumber of molelcules
Total (without water)78,51010
Polymers78,51010
Non-polymers00
Water2,306128
1
A: Gamma-aminobutyric acid receptor-associated protein
B: Tumor protein p53-inducible nuclear protein 2


Theoretical massNumber of molelcules
Total (without water)15,7022
Polymers15,7022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-9 kcal/mol
Surface area7560 Å2
MethodPISA
2
C: Gamma-aminobutyric acid receptor-associated protein
D: Tumor protein p53-inducible nuclear protein 2


Theoretical massNumber of molelcules
Total (without water)15,7022
Polymers15,7022
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-6 kcal/mol
Surface area7220 Å2
MethodPISA
3
E: Gamma-aminobutyric acid receptor-associated protein
F: Tumor protein p53-inducible nuclear protein 2


Theoretical massNumber of molelcules
Total (without water)15,7022
Polymers15,7022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-9 kcal/mol
Surface area7210 Å2
MethodPISA
4
G: Gamma-aminobutyric acid receptor-associated protein
H: Tumor protein p53-inducible nuclear protein 2


Theoretical massNumber of molelcules
Total (without water)15,7022
Polymers15,7022
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-8 kcal/mol
Surface area6990 Å2
MethodPISA
5
I: Gamma-aminobutyric acid receptor-associated protein
J: Tumor protein p53-inducible nuclear protein 2


Theoretical massNumber of molelcules
Total (without water)15,7022
Polymers15,7022
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-8 kcal/mol
Surface area6970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.898, 95.783, 138.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 11 or resid 13...
21(chain C and (resid 2 through 11 or resid 13...
31(chain E and (resid 2 through 11 or resid 13...
41(chain G and (resid 2 through 11 or resid 13...
51(chain I and (resid 2 through 11 or resid 13...
12(chain B and resid 29 through 41)
22chain F

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
111LYSLYSPHEPHE(chain A and (resid 2 through 11 or resid 13...AA2 - 114 - 13
121LYSLYSALAALA(chain A and (resid 2 through 11 or resid 13...AA13 - 3915 - 41
131ILEILELEULEU(chain A and (resid 2 through 11 or resid 13...AA41 - 7043 - 72
141ALAALAGLYGLY(chain A and (resid 2 through 11 or resid 13...AA72 - 9274 - 94
161HISHISVALVAL(chain A and (resid 2 through 11 or resid 13...AA98 - 114100 - 116
211LYSLYSPHEPHE(chain C and (resid 2 through 11 or resid 13...CC2 - 114 - 13
221LYSLYSALAALA(chain C and (resid 2 through 11 or resid 13...CC13 - 3915 - 41
231ILEILELEULEU(chain C and (resid 2 through 11 or resid 13...CC41 - 7043 - 72
241ALAALAALAALA(chain C and (resid 2 through 11 or resid 13...CC7274
251HISHISVALVAL(chain C and (resid 2 through 11 or resid 13...CC98 - 114100 - 116
311LYSLYSPHEPHE(chain E and (resid 2 through 11 or resid 13...EE2 - 114 - 13
321LYSLYSALAALA(chain E and (resid 2 through 11 or resid 13...EE13 - 3915 - 41
331ILEILELEULEU(chain E and (resid 2 through 11 or resid 13...EE41 - 7043 - 72
341ALAALAGLYGLY(chain E and (resid 2 through 11 or resid 13...EE72 - 9274 - 94
351LEULEUTYRTYR(chain E and (resid 2 through 11 or resid 13...EE94 - 9596 - 97
361HISHISVALVAL(chain E and (resid 2 through 11 or resid 13...EE98 - 114100 - 116
411LYSLYSPHEPHE(chain G and (resid 2 through 11 or resid 13...GG2 - 114 - 13
421LYSLYSALAALA(chain G and (resid 2 through 11 or resid 13...GG13 - 3915 - 41
431ILEILELEULEU(chain G and (resid 2 through 11 or resid 13...GG41 - 7043 - 72
441ALAALAGLYGLY(chain G and (resid 2 through 11 or resid 13...GG72 - 9274 - 94
461HISHISVALVAL(chain G and (resid 2 through 11 or resid 13...GG98 - 114100 - 116
511LYSLYSPHEPHE(chain I and (resid 2 through 11 or resid 13...II2 - 114 - 13
521LYSLYSALAALA(chain I and (resid 2 through 11 or resid 13...II13 - 3915 - 41
531ILEILELEULEU(chain I and (resid 2 through 11 or resid 13...II41 - 7043 - 72
541ALAALAGLYGLY(chain I and (resid 2 through 11 or resid 13...II72 - 9274 - 94
551LEULEUTYRTYR(chain I and (resid 2 through 11 or resid 13...II94 - 9596 - 97
561HISHISVALVAL(chain I and (resid 2 through 11 or resid 13...II98 - 114100 - 116
112GLYGLYPROPRO(chain B and resid 29 through 41)BB29 - 411 - 13
212GLYGLYPROPROchain FFF29 - 411 - 13

NCS ensembles :
ID
1
2

-
Components

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


Mass: 14086.176 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAP, FLC3B, HT004 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O95166
#2: Protein/peptide
Tumor protein p53-inducible nuclear protein 2 / Diabetes and obesity-regulated gene / p53-inducible protein U / PIG-U


Mass: 1615.738 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53INP2, C20orf110, DOR, PINH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IXH6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG3350, 0.1M Na-citrate, 5% isopropanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 2.096→26.253 Å / Num. obs: 37232 / % possible obs: 90.03 % / Redundancy: 5.2 % / CC1/2: 0.997 / Net I/σ(I): 10.78
Reflection shellResolution: 2.096→2.171 Å / Num. unique obs: 1455 / CC1/2: 0.222

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.096→26.253 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 2000 5.37 %
Rwork0.197 35213 -
obs0.2005 37213 90.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.67 Å2 / Biso mean: 57.1633 Å2 / Biso min: 22.02 Å2
Refinement stepCycle: final / Resolution: 2.096→26.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5242 0 0 128 5370
Biso mean---51.53 -
Num. residues----624
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2689X-RAY DIFFRACTION6.842TORSIONAL
12C2689X-RAY DIFFRACTION6.842TORSIONAL
13E2689X-RAY DIFFRACTION6.842TORSIONAL
14G2689X-RAY DIFFRACTION6.842TORSIONAL
15I2689X-RAY DIFFRACTION6.842TORSIONAL
21B116X-RAY DIFFRACTION6.842TORSIONAL
22F116X-RAY DIFFRACTION6.842TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0963-2.14870.329460.326181230
2.1487-2.20680.37870.3099154156
2.2068-2.27170.35631280.2988223380
2.2717-2.34490.34391460.2872258794
2.3449-2.42870.33221530.2578269999
2.4287-2.52590.32361580.24762768100
2.5259-2.64070.31751570.24012759100
2.6407-2.77980.30831580.21832773100
2.7798-2.95370.30851570.2212782100
2.9537-3.18140.27611580.21012788100
3.1814-3.50090.25821600.19292802100
3.5009-4.0060.23921600.1762834100
4.006-5.04130.20611620.14852847100
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)
11.31460.4924-0.79281.93941.05391.4330.0701-0.11890.21850.5782-0.35990.4148-0.7417-0.10890.00020.39470.0585-0.01480.4173-0.02810.4033-9.43833.06729.1727
22.32390.07220.01721.90450.61582.9232-0.02060.37670.0034-0.1464-0.07750.2523-0.1709-0.1141-00.2496-0.030.0120.30320.00420.3545-6.7806-5.746916.0576
30.5266-0.7542.13231.1222-3.14688.8488-0.29950.68570.19210.3118-0.15350.4634-0.8528-0.6439-0.31260.1439-0.05440.05850.4497-0.14940.624-17.6453-8.860926.8885
40.1179-0.4199-0.49151.70492.30763.5934-0.1277-0.2546-1.1211-0.15270.12050.08091.52860.99720.03310.5170.05290.0610.3455-0.05470.6165-10.2494-20.076621.1942
50.5303-0.0701-0.29190.2631-0.25320.45270.0642-0.16250.62930.12940.4584-1.2201-0.11961.08890.0020.6320.01720.01930.5195-0.02790.427111.21924.840630.8823
60.5144-0.09670.44761.43650.2090.4224-0.1663-0.48190.31160.9909-0.44560.6115-0.1578-0.3583-0.03920.47220.0697-0.05050.3812-0.05770.54152.464315.996535.208
70.8789-0.21260.14021.3513-0.55420.83260.06950.42450.749-0.4696-0.1434-0.715-0.59230.6022-0.09610.4927-0.0951-0.09690.3355-0.0660.520410.351218.941526.5613
80.95260.9027-1.07031.1621-0.71381.9692-0.4054-0.47980.5258-0.02950.4093-0.3842-0.670.3348-0.0030.4588-0.0348-0.07150.5918-0.06730.532417.509114.540222.6207
91.9079-1.9340.71995.24532.6923.8061.32050.10610.319-1.81090.4935-0.17260.11331.00980.99920.7475-0.26170.03030.6347-0.00370.47319.000719.841816.9263
100.6999-0.755-0.08120.8999-0.26420.9116-0.29890.77180.1735-0.26570.2519-0.25810.02530.62640.00040.3572-0.11520.04930.71210.02890.503316.895713.214113.4454
110.3669-0.0063-0.45960.06480.02890.5771-0.0140.5751-0.1768-0.64280.08980.45060.2904-1.08350.00450.4121-0.07770.00990.37170.0090.44652.967617.494518.4461
120.74160.23430.89650.69180.01481.1044-0.0763-0.0544-0.1340.0898-0.0008-0.148-0.11610.37970.00140.3834-0.0009-0.03520.308-0.02460.36517.045611.578124.9097
130.0786-0.05340.05710.1240.04660.1605-0.2726-1.188-1.4018-0.52590.433-0.6088-0.17740.81170.00460.65560.0115-0.05560.68720.07060.775617.7073.116313.3032
143.3376-2.3092-2.36961.6131.66261.7073-0.99340.02720.80030.08750.7595-0.0018-0.01730.9134-0.02230.7635-0.1824-0.08840.4888-0.0340.687815.273223.268831.237
150.32230.09270.1950.67910.57060.47890.6064-1.3311-0.29720.6685-0.1107-0.40690.88640.92820.02220.35830.0315-0.16230.5244-0.02830.536620.8163-16.020546.4111
161.6879-1.66520.89541.8311-1.35031.6812-0.553-0.05580.4343-0.14180.768-1.04-1.19940.67150.05720.5327-0.2101-0.04010.5047-0.11810.61522.3015-3.17839.6018
172.77520.74671.70371.87681.53722.39330.14140.1048-0.3123-0.2404-0.2501-0.57130.2290.1719-0.0020.2523-0.0557-0.02160.34050.08070.485517.6283-19.511535.9922
180.0793-0.03520.09780.46630.20580.22820.10490.28590.3965-0.0598-0.0436-0.1952-0.27440.24400.2969-0.0070.04140.38250.02680.403514.4703-12.861628.4203
190.11450.0152-0.25630.4960.02470.4386-0.0005-0.1487-0.4714-0.63010.2309-0.02030.7834-0.0163-0.0010.44550.0049-0.05360.34890.06260.446312.6183-23.498428.2784
201.6629-1.9825-0.13522.20010.53593.6121-0.2861-0.2845-0.40340.3550.19330.48181.3103-0.1667-0.02890.4521-0.11440.00760.46520.0780.4556.9139-23.967634.3216
211.21910.42051.0171.0803-0.91672.1376-0.0072-0.3518-0.13380.3976-0.020.06950.1145-0.40130.00030.3666-0.0407-0.01720.40050.0130.366210.4105-14.747639.7027
223.23961.60033.32492.33090.17014.59110.35031.1124-0.8706-0.23460.4226-1.09570.76360.74060.21440.2879-0.08580.07320.4934-0.13940.540322.2663-13.524826.557
230.3309-0.0260.05770.1924-0.2080.2151-0.0047-0.2718-0.09530.0769-0.50020.46490.50260.16970.00270.445-0.01320.0160.5861-0.00110.366812.4725-6.591752.4747
240.742-0.2003-1.40832.7878-0.45172.9343-0.2038-0.03830.21780.43720.06470.141-1.3391-2.1566-0.74670.76810.327-0.11670.90330.10320.31590.00091.071549.5862
252.0954-0.76760.70040.6911-0.30240.24570.25090.6810.7448-0.0949-0.41740.1681-0.2231-1.5472-0.09880.27530.2937-0.0730.9139-0.01780.4231-0.5294-5.666859.2473
261.11730.63840.22561.0135-1.22293.16110.3478-0.7256-0.3921-0.0868-0.31740.11010.7083-0.8703-0.0010.5637-0.0314-0.06910.6857-0.04510.47773.6993-12.865965.3788
271.3297-0.26920.11540.57690.48521.5560.3214-0.1814-0.44550.2765-0.34090.1342-0.0085-0.8781-00.6704-0.0834-0.08410.53540.01830.46028.1519-10.0671.7387
284.39972.3011-1.6041.2989-0.92140.65370.1898-0.56690.1934-0.6863-1.06250.3119-2.4143-0.564-0.12111.01480.2357-0.03030.585-0.04180.571.73742.520265.788
290.7096-0.5295-0.90490.52960.45011.15770.2097-0.4666-0.29750.13040.03590.46920.0834-0.9570.00360.58810.0305-0.06640.4402-0.03930.44476.762-1.922659.1614
300.072-0.0110.01460.0917-0.060.0362-0.1867-0.3884-0.9072-0.25160.8818-1.58660.0391-0.10270.00510.7463-0.0079-0.16790.87670.07430.811317.8516-10.505770.904
310.188-0.2304-0.09520.2750.11480.04540.96680.5639-0.4546-0.2537-0.6384-0.789-0.8818-0.27510.01720.5785-0.0998-0.04090.9350.09820.4445-5.0455-10.981758.1547
320.2783-0.13870.2740.1373-0.06980.274-0.71010.0550.6611-0.39410.96650.1289-0.4413-0.10250.00130.840.051-0.17570.53030.06140.911810.993516.160258.8869
333.41141.4389-0.26150.94080.16180.2073-0.30381.72690.4663-1.52030.20090.34730.3092-0.193-0.01161.0711-0.0099-0.07540.68860.10620.373715.720711.952945.8527
343.11950.33181.2922.2856-0.58912.4507-0.26990.28830.2085-0.5953-0.1393-0.0142-0.97950.88380.00060.7807-0.0458-0.06180.6330.13380.610626.385216.301560.732
352.481-1.15720.90633.5435-2.59412.62680.08730.0533-0.1067-0.3812-0.1405-0.0240.15080.21250.00030.5004-0.0278-0.07130.43190.02020.477623.80499.520864.0672
360.00510.17730.05915.3421.70160.54210.05320.90530.1954-0.75430.02-1.3937-0.51290.49310.13750.7675-0.35490.10811.03850.13150.612528.821619.229951.9756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )A1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 114 )A25 - 114
3X-RAY DIFFRACTION3chain 'B' and (resid 29 through 37 )B29 - 37
4X-RAY DIFFRACTION4chain 'B' and (resid 38 through 42 )B38 - 42
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 10 )C1 - 10
6X-RAY DIFFRACTION6chain 'C' and (resid 11 through 24 )C11 - 24
7X-RAY DIFFRACTION7chain 'C' and (resid 25 through 35 )C25 - 35
8X-RAY DIFFRACTION8chain 'C' and (resid 36 through 56 )C36 - 56
9X-RAY DIFFRACTION9chain 'C' and (resid 57 through 67 )C57 - 67
10X-RAY DIFFRACTION10chain 'C' and (resid 68 through 90 )C68 - 90
11X-RAY DIFFRACTION11chain 'C' and (resid 91 through 98 )C91 - 98
12X-RAY DIFFRACTION12chain 'C' and (resid 99 through 110 )C99 - 110
13X-RAY DIFFRACTION13chain 'C' and (resid 111 through 116 )C111 - 116
14X-RAY DIFFRACTION14chain 'D' and (resid 31 through 39 )D31 - 39
15X-RAY DIFFRACTION15chain 'E' and (resid 1 through 10 )E1 - 10
16X-RAY DIFFRACTION16chain 'E' and (resid 11 through 24 )E11 - 24
17X-RAY DIFFRACTION17chain 'E' and (resid 25 through 47 )E25 - 47
18X-RAY DIFFRACTION18chain 'E' and (resid 48 through 56 )E48 - 56
19X-RAY DIFFRACTION19chain 'E' and (resid 57 through 68 )E57 - 68
20X-RAY DIFFRACTION20chain 'E' and (resid 69 through 90 )E69 - 90
21X-RAY DIFFRACTION21chain 'E' and (resid 91 through 117 )E91 - 117
22X-RAY DIFFRACTION22chain 'F' and (resid 29 through 41 )F29 - 41
23X-RAY DIFFRACTION23chain 'G' and (resid 1 through 10 )G1 - 10
24X-RAY DIFFRACTION24chain 'G' and (resid 11 through 24 )G11 - 24
25X-RAY DIFFRACTION25chain 'G' and (resid 25 through 35 )G25 - 35
26X-RAY DIFFRACTION26chain 'G' and (resid 36 through 68 )G36 - 68
27X-RAY DIFFRACTION27chain 'G' and (resid 69 through 90 )G69 - 90
28X-RAY DIFFRACTION28chain 'G' and (resid 91 through 98 )G91 - 98
29X-RAY DIFFRACTION29chain 'G' and (resid 99 through 110 )G99 - 110
30X-RAY DIFFRACTION30chain 'G' and (resid 111 through 116 )G111 - 116
31X-RAY DIFFRACTION31chain 'H' and (resid 34 through 39 )H34 - 39
32X-RAY DIFFRACTION32chain 'I' and (resid 1 through 10 )I1 - 10
33X-RAY DIFFRACTION33chain 'I' and (resid 11 through 24 )I11 - 24
34X-RAY DIFFRACTION34chain 'I' and (resid 25 through 68 )I25 - 68
35X-RAY DIFFRACTION35chain 'I' and (resid 69 through 114 )I69 - 114
36X-RAY DIFFRACTION36chain 'J' and (resid 35 through 39 )J35 - 39

+
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