[English] 日本語
Yorodumi
- PDB-5npw: Structure of human ATG5-ATG16L1(ATG5BD) complex (C2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5npw
TitleStructure of human ATG5-ATG16L1(ATG5BD) complex (C2)
Components
  • Autophagy protein 5
  • Autophagy-related protein 16-1
KeywordsCELL CYCLE / autophagy / ATG16L1 / ATG5
Function / homology
Function and homology information


otolith development / regulation of autophagosome maturation / response to fluoride / regulation of cytokine production involved in immune response / positive regulation of viral translation / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / antigen processing and presentation of endogenous antigen / C-terminal protein lipidation / negative regulation of autophagic cell death ...otolith development / regulation of autophagosome maturation / response to fluoride / regulation of cytokine production involved in immune response / positive regulation of viral translation / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / antigen processing and presentation of endogenous antigen / C-terminal protein lipidation / negative regulation of autophagic cell death / cellular response to nitrosative stress / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / ventricular cardiac muscle cell development / microautophagy / mitochondria-associated endoplasmic reticulum membrane contact site / regulation of cilium assembly / aggrephagy / transferase complex / mucus secretion / response to fungus / xenophagy / nucleophagy / negative thymic T cell selection / protein localization to phagophore assembly site / corpus callosum development / phagophore assembly site membrane / cellular response to nitrogen starvation / negative stranded viral RNA replication / regulation of release of sequestered calcium ion into cytosol / endolysosome membrane / negative regulation of phagocytosis / response to iron(II) ion / positive regulation of mucus secretion / negative regulation of cardiac muscle cell apoptotic process / negative regulation of type I interferon production / Macroautophagy / chaperone-mediated autophagy / Receptor Mediated Mitophagy / heart contraction / axoneme / autophagosome membrane / mitophagy / autophagosome assembly / autophagosome / negative regulation of reactive oxygen species metabolic process / blood vessel remodeling / positive regulation of autophagy / protein-membrane adaptor activity / negative regulation of protein ubiquitination / cardiac muscle cell apoptotic process / sperm midpiece / PINK1-PRKN Mediated Mitophagy / negative regulation of innate immune response / post-translational protein modification / Negative regulators of DDX58/IFIH1 signaling / establishment of localization in cell / hippocampus development / macroautophagy / autophagy / vasodilation / phagocytic vesicle membrane / protein transport / GTPase binding / chromatin organization / defense response to virus / protein ubiquitination / response to xenobiotic stimulus / axon / protein-containing complex / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / : / : / : / Autophagy protein ATG5, alpha-helical bundle region / Autophagy protein ATG5, UblA domain / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain ...Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / : / : / : / Autophagy protein ATG5, alpha-helical bundle region / Autophagy protein ATG5, UblA domain / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / Autophagy protein ATG5, UblB domain / Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / Serum Albumin; Chain A, Domain 1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Autophagy-related protein 16-1 / Autophagy protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsArchna, A. / Scrima, A.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Identification, biochemical characterization and crystallization of the central region of human ATG16L1.
Authors: Archna, A. / Scrima, A.
History
DepositionApr 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Autophagy protein 5
B: Autophagy-related protein 16-1
C: Autophagy protein 5
D: Autophagy-related protein 16-1
E: Autophagy protein 5
F: Autophagy-related protein 16-1
G: Autophagy protein 5
H: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)271,9118
Polymers271,9118
Non-polymers00
Water1267
1
A: Autophagy protein 5
B: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)67,9782
Polymers67,9782
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-18 kcal/mol
Surface area14910 Å2
MethodPISA
2
C: Autophagy protein 5
D: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)67,9782
Polymers67,9782
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-13 kcal/mol
Surface area14770 Å2
MethodPISA
3
E: Autophagy protein 5
F: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)67,9782
Polymers67,9782
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-18 kcal/mol
Surface area14640 Å2
MethodPISA
4
G: Autophagy protein 5
H: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)67,9782
Polymers67,9782
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-14 kcal/mol
Surface area14850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.860, 75.990, 142.440
Angle α, β, γ (deg.)90.000, 131.410, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 4 or (resid 5 and (name...
21(chain C and ((resid 4 and (name N or name...
31(chain E and ((resid 4 and (name N or name...
41(chain G and ((resid 4 and (name N or name...
12(chain D and ((resid 10 and (name N or name...
22(chain B and ((resid 10 and (name N or name...
32(chain F and (resseq 10:14 or (resid 15 and (name...
42(chain H and ((resid 10 and (name N or name...

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
111ASPASPASPASP(chain A and (resseq 4 or (resid 5 and (name...AA411
121LYSLYSLYSLYS(chain A and (resseq 4 or (resid 5 and (name...AA512
131ASPASPASPASP(chain A and (resseq 4 or (resid 5 and (name...AA4 - 27511 - 282
141ASPASPASPASP(chain A and (resseq 4 or (resid 5 and (name...AA4 - 27511 - 282
151ASPASPASPASP(chain A and (resseq 4 or (resid 5 and (name...AA4 - 27511 - 282
161ASPASPASPASP(chain A and (resseq 4 or (resid 5 and (name...AA4 - 27511 - 282
171ASPASPASPASP(chain A and (resseq 4 or (resid 5 and (name...AA4 - 27511 - 282
181ASPASPASPASP(chain A and (resseq 4 or (resid 5 and (name...AA4 - 27511 - 282
211ASPASPASPASP(chain C and ((resid 4 and (name N or name...CC411
221METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
231METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
241METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
251METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
261METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
271METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
281METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
291METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
2101METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
2111METMETTHRTHR(chain C and ((resid 4 and (name N or name...CC1 - 2748 - 281
311ASPASPASPASP(chain E and ((resid 4 and (name N or name...EE411
321ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
331ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
341ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
351ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
361ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
371ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
381ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
391ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
3101ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
3111ASPASPTHRTHR(chain E and ((resid 4 and (name N or name...EE3 - 27410 - 281
411ASPASPASPASP(chain G and ((resid 4 and (name N or name...GG411
421METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
431METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
441METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
451METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
461METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
471METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
481METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
491METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
4101METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
4111METMETASPASP(chain G and ((resid 4 and (name N or name...GG1 - 2758 - 282
112ARGARGARGARG(chain D and ((resid 10 and (name N or name...DD104
122GLYGLYASPASP(chain D and ((resid 10 and (name N or name...DD8 - 472 - 41
132GLYGLYASPASP(chain D and ((resid 10 and (name N or name...DD8 - 472 - 41
142GLYGLYASPASP(chain D and ((resid 10 and (name N or name...DD8 - 472 - 41
152GLYGLYASPASP(chain D and ((resid 10 and (name N or name...DD8 - 472 - 41
162GLYGLYASPASP(chain D and ((resid 10 and (name N or name...DD8 - 472 - 41
212ARGARGARGARG(chain B and ((resid 10 and (name N or name...BB104
222GLYGLYLEULEU(chain B and ((resid 10 and (name N or name...BB9 - 483 - 42
232GLYGLYLEULEU(chain B and ((resid 10 and (name N or name...BB9 - 483 - 42
242GLYGLYLEULEU(chain B and ((resid 10 and (name N or name...BB9 - 483 - 42
252GLYGLYLEULEU(chain B and ((resid 10 and (name N or name...BB9 - 483 - 42
262GLYGLYLEULEU(chain B and ((resid 10 and (name N or name...BB9 - 483 - 42
312ARGARGLYSLYS(chain F and (resseq 10:14 or (resid 15 and (name...FF10 - 144 - 8
322ARGARGARGARG(chain F and (resseq 10:14 or (resid 15 and (name...FF159
332ARGARGLEULEU(chain F and (resseq 10:14 or (resid 15 and (name...FF10 - 484 - 42
342ARGARGLEULEU(chain F and (resseq 10:14 or (resid 15 and (name...FF10 - 484 - 42
352ARGARGLEULEU(chain F and (resseq 10:14 or (resid 15 and (name...FF10 - 484 - 42
362ARGARGLEULEU(chain F and (resseq 10:14 or (resid 15 and (name...FF10 - 484 - 42
372ARGARGLEULEU(chain F and (resseq 10:14 or (resid 15 and (name...FF10 - 484 - 42
382ARGARGLEULEU(chain F and (resseq 10:14 or (resid 15 and (name...FF10 - 484 - 42
412ARGARGARGARG(chain H and ((resid 10 and (name N or name...HH104
422GLYGLYLEULEU(chain H and ((resid 10 and (name N or name...HH8 - 482 - 42
432GLYGLYLEULEU(chain H and ((resid 10 and (name N or name...HH8 - 482 - 42
442GLYGLYLEULEU(chain H and ((resid 10 and (name N or name...HH8 - 482 - 42
452GLYGLYLEULEU(chain H and ((resid 10 and (name N or name...HH8 - 482 - 42
462GLYGLYLEULEU(chain H and ((resid 10 and (name N or name...HH8 - 482 - 42

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Autophagy protein 5 / / APG5-like / Apoptosis-specific protein


Mass: 33187.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG5, APG5L, ASP / Plasmid: pET15b-derived / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H1Y0
#2: Protein
Autophagy-related protein 16-1 / APG16-like 1


Mass: 34789.879 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG16L1, APG16L, UNQ9393/PRO34307 / Plasmid: pCOLA-derived / Production host: Escherichia coli (E. coli) / References: UniProt: Q676U5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.4 M KCl and 18 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→48.316 Å / Num. obs: 29428 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.698 % / Biso Wilson estimate: 62.2 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.147 / Χ2: 0.962 / Net I/σ(I): 9.48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.23.8410.7452.0826430.6870.86599.3
3.2-3.33.7980.5043.0423660.8260.58699.3
3.3-43.5760.2285.9106140.9560.26899.2
4-63.8260.09412.9896460.990.10999.1
6-103.5050.0616.3232300.9960.0798.9
10-48.3163.7710.03727.669290.9970.04396.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GDK

4gdk


Resolution: 3.1→48.316 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.52
RfactorNum. reflection% reflection
Rfree0.2639 1472 5 %
Rwork0.2175 --
obs0.2198 29416 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 206.4 Å2 / Biso mean: 68.1332 Å2 / Biso min: 4.46 Å2
Refinement stepCycle: final / Resolution: 3.1→48.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9945 0 0 7 9952
Biso mean---18.24 -
Num. residues----1221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310225
X-RAY DIFFRACTIONf_angle_d0.50413895
X-RAY DIFFRACTIONf_chiral_restr0.0391499
X-RAY DIFFRACTIONf_plane_restr0.0031783
X-RAY DIFFRACTIONf_dihedral_angle_d8.9636104
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5734X-RAY DIFFRACTION5.965TORSIONAL
12C5734X-RAY DIFFRACTION5.965TORSIONAL
13E5734X-RAY DIFFRACTION5.965TORSIONAL
14G5734X-RAY DIFFRACTION5.965TORSIONAL
21D812X-RAY DIFFRACTION5.965TORSIONAL
22B812X-RAY DIFFRACTION5.965TORSIONAL
23F812X-RAY DIFFRACTION5.965TORSIONAL
24H812X-RAY DIFFRACTION5.965TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1001-3.20020.37091330.357525132646
3.2002-3.31450.34311330.294425352668
3.3145-3.44720.33451330.286925332666
3.4472-3.6040.29821320.254825022634
3.604-3.7940.28491340.223725372671
3.794-4.03160.26251320.207525162648
4.0316-4.34270.24171340.190125392673
4.3427-4.77940.20441330.165125302663
4.7794-5.47010.23621340.182925552689
5.4701-6.88860.26771350.229225522687
6.8886-48.32190.24261390.197426322771
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)
11.92740.12670.86731.72770.72664.7994-0.0657-0.01270.1704-0.11820.1835-0.1911-0.4669-0.021-0.12130.37770.0630.03950.4420.03410.4205-61.8908-5.8694118.2184
23.9635-1.48271.17952.8216-0.96814.8322-0.07870.108-0.2933-0.18860.15350.05240.28290.025-0.05840.48640.0060.10110.4712-0.02030.3993-61.8931-26.26110.7073
32.6275-0.09190.00097.52763.60325.2194-0.5016-0.2914-0.08770.46830.12170.79830.3745-0.460.4280.3982-0.06690.0060.57020.03010.5086-71.6716-16.9182129.4802
41.57490.0753-0.3912.1651.93016.88650.1085-0.09640.14340.0384-0.1834-0.0685-0.05230.14680.03160.3669-0.02830.0210.43080.02570.4242-48.9649-16.161588.1377
52.6259-0.80030.25383.7756-0.19652.04830.0188-0.15080.0443-0.07610.0011-0.14770.02620.1701-0.0070.3768-0.0057-0.04110.3707-0.03560.3651-41.9863-31.616872.5577
61.5104-2.2164-2.74325.5825.08175.3982-0.14410.05290.0074-0.15410.06160.4332-0.1439-0.12580.06190.5358-0.0086-0.14710.55110.09120.4721-59.4183-17.010173.2412
73.5685-1.302-0.48210.6140.762.61530.0827-0.2048-0.58220.0111-0.1297-0.230.61750.57570.37220.5987-0.0843-0.10760.3720.15680.3394-80.7059-17.522385.4974
84.42021.95211.13965.8574-1.2023.2531-0.00970.43310.63570.11730.1380.4541-0.3254-0.0546-0.10630.4331-0.04570.06430.47840.09060.4616-80.019-2.228574.339
93.69950.14860.22823.79362.29294.84360.0285-0.2036-0.23870.1066-0.30730.27860.0848-0.29030.27280.4387-0.00690.04640.48770.01480.5099-94.9717-23.132578.8527
106.06624.9134-0.30054.0993-0.30923.43330.40570.2546-2.01051.28250.0302-1.12010.42680.2841-0.40360.72960.1277-0.0460.5362-0.01330.8826-77.8185-30.397183.3097
113.8412-2.2462-0.43632.43671.20016.7899-0.5345-0.6060.16471.01091.1215-0.5248-0.1279-0.1391-0.53660.41930.08190.06940.5938-0.00570.4705-67.6853-5.47888.561
128.4896-2.11582.36013.1897-0.40472.84730.1138-0.49890.45060.2014-0.20.1486-0.1433-0.55820.11220.5104-0.0375-0.00830.5188-0.00110.4143-75.447-12.4204152.5049
1330.4228-0.51013.1809-0.34423.34230.15-0.1357-0.1490.2109-0.2443-0.32770.12160.11940.07570.3701-0.0551-0.03290.37140.10110.4743-60.1964-25.8383162.2421
143.4961-1.50732.91984.8782-1.23366.04810.41970.4979-0.6977-0.61890.1835-0.92060.11330.1629-0.47980.50960.02380.09870.34520.08610.8098-52.2309-23.571145.4839
156.1462-0.46882.18172.4466-2.77966.26870.2325-0.88110.21890.3324-0.23210.176-0.68651.14190.07140.46990.00980.00570.5815-0.02570.5161-68.9196-0.5406140.8652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 136 )A4 - 136
2X-RAY DIFFRACTION2chain 'A' and (resid 137 through 275 )A137 - 275
3X-RAY DIFFRACTION3chain 'B' and (resid 9 through 48 )B9 - 48
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 117 )C1 - 117
5X-RAY DIFFRACTION5chain 'C' and (resid 118 through 274 )C118 - 274
6X-RAY DIFFRACTION6chain 'D' and (resid 8 through 47 )D8 - 47
7X-RAY DIFFRACTION7chain 'E' and (resid 3 through 22 )E3 - 22
8X-RAY DIFFRACTION8chain 'E' and (resid 23 through 117 )E23 - 117
9X-RAY DIFFRACTION9chain 'E' and (resid 118 through 274 )E118 - 274
10X-RAY DIFFRACTION10chain 'F' and (resid 10 through 28 )F10 - 28
11X-RAY DIFFRACTION11chain 'F' and (resid 29 through 48 )F29 - 48
12X-RAY DIFFRACTION12chain 'G' and (resid 1 through 117 )G1 - 117
13X-RAY DIFFRACTION13chain 'G' and (resid 118 through 275 )G118 - 275
14X-RAY DIFFRACTION14chain 'H' and (resid 8 through 28 )H8 - 28
15X-RAY DIFFRACTION15chain 'H' and (resid 29 through 48 )H29 - 48

+
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