[English] 日本語
Yorodumi
- PDB-6hoh: Structure of VPS34 LIR motif (S249E) bound to GABARAP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hoh
TitleStructure of VPS34 LIR motif (S249E) bound to GABARAP
ComponentsPhosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
KeywordsSIGNALING PROTEIN / Autophagy / ATG8 / LIR
Function / homology
Function and homology information


positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation of protein K48-linked ubiquitination / presynaptic endosome ...positive regulation of protein lipidation / postsynaptic endosome / Toll Like Receptor 9 (TLR9) Cascade / Synthesis of PIPs at the late endosome membrane / phosphatidylinositol 3-kinase complex, class III / Synthesis of PIPs at the early endosome membrane / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / positive regulation of protein K48-linked ubiquitination / presynaptic endosome / host-mediated activation of viral genome replication / regulation of Rac protein signal transduction / phosphatidylinositol kinase activity / Synthesis of PIPs at the Golgi membrane / early endosome to late endosome transport / response to L-leucine / protein localization to phagophore assembly site / protein targeting to lysosome / endosome organization / pexophagy / GABA receptor binding / positive regulation of natural killer cell mediated cytotoxicity / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / phagophore assembly site / TBC/RABGAPs / cellular response to nitrogen starvation / phosphatidylinositol 3-kinase / microtubule associated complex / phosphatidylinositol-3-phosphate biosynthetic process / 1-phosphatidylinositol-3-kinase activity / Macroautophagy / phosphatidylinositol phosphate biosynthetic process / phosphatidylinositol-mediated signaling / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / smooth endoplasmic reticulum / autolysosome / autophagosome membrane / PI3K Cascade / extrinsic apoptotic signaling pathway via death domain receptors / RHO GTPases Activate NADPH Oxidases / regulation of macroautophagy / autophagosome maturation / axoneme / autophagosome assembly / synaptic vesicle endocytosis / beta-tubulin binding / protein targeting / cellular response to glucose starvation / mitophagy / autophagosome / regulation of cytokinesis / regulation of autophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein processing / GABA-ergic synapse / microtubule cytoskeleton organization / autophagy / endocytosis / phagocytic vesicle membrane / peroxisome / late endosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / sperm midpiece / cytoplasmic vesicle / midbody / Translation of Replicase and Assembly of the Replication Transcription Complex / microtubule binding / intracellular membrane-bounded organelle / chemical synaptic transmission / microtubule / protein kinase activity / lysosome / endosome / Golgi membrane / cell division / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / glutamatergic synapse / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Phosphatidylinositol 3-kinase, Vps34 type / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) ...: / Phosphatidylinositol 3-kinase, Vps34 type / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / C2 domain superfamily / Ubiquitin-like (UB roll) / Armadillo-type fold / Ubiquitin-like domain superfamily / Roll / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Gamma-aminobutyric acid receptor-associated protein / Phosphatidylinositol 3-kinase catalytic subunit type 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMouilleron, S. / Birgisdottir, A.B. / Bhujbal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S. ...Mouilleron, S. / Birgisdottir, A.B. / Bhujbal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S. / Lamark, T. / Johansen, T.
Funding support Norway, 2items
OrganizationGrant numberCountry
Research Council of Norway214448 Norway
Research Council of Norway249884 Norway
CitationJournal: Autophagy / Year: 2019
Title: Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs.
Authors: Birgisdottir, A.B. / Mouilleron, S. / Bhujabal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S.A. / Lamark, T. / Johansen, T.
History
DepositionSep 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
B: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
C: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
D: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0845
Polymers60,9344
Non-polymers1501
Water2,882160
1
A: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
hetero molecules

A: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
hetero molecules

A: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1516
Polymers45,7013
Non-polymers4513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6650 Å2
ΔGint-26 kcal/mol
Surface area19790 Å2
MethodPISA
2
B: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein
C: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein

D: Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein


Theoretical massNumber of molelcules
Total (without water)45,7013
Polymers45,7013
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
Buried area5870 Å2
ΔGint-43 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.502, 119.502, 119.502
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

-
Components

#1: Protein
Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein / PtdIns-3-kinase type 3 / Phosphatidylinositol 3-kinase p100 subunit / Phosphoinositide-3-kinase ...PtdIns-3-kinase type 3 / Phosphatidylinositol 3-kinase p100 subunit / Phosphoinositide-3-kinase class 3 / hVps34 / GABA(A) receptor-associated protein / MM46


Mass: 15233.520 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIK3C3, VPS34, GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NEB9, UniProt: O95166, phosphatidylinositol 3-kinase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 200 mM magnesium formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.25→53.443 Å / Num. obs: 27219 / % possible obs: 99.49 % / Redundancy: 5.8 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Net I/σ(I): 10.4
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.98 / Num. unique obs: 2654 / CC1/2: 0.65 / Rpim(I) all: 0.44 / Rrim(I) all: 1.07 / Χ2: 39 / % possible all: 99.21

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GNU

1gnu


Resolution: 2.25→53.44 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.25
RfactorNum. reflection% reflection
Rfree0.2496 1272 4.7 %
Rwork0.2064 --
obs0.2084 27048 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→53.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4153 0 10 160 4323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024320
X-RAY DIFFRACTIONf_angle_d0.4225843
X-RAY DIFFRACTIONf_dihedral_angle_d16.4792636
X-RAY DIFFRACTIONf_chiral_restr0.044616
X-RAY DIFFRACTIONf_plane_restr0.003761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2504-2.34050.37711310.34392813X-RAY DIFFRACTION99
2.3405-2.4470.42951610.32822774X-RAY DIFFRACTION99
2.447-2.5760.35781500.30942812X-RAY DIFFRACTION99
2.576-2.73740.31871340.28712870X-RAY DIFFRACTION100
2.7374-2.94870.29761350.25762843X-RAY DIFFRACTION100
2.9487-3.24540.32021460.21742881X-RAY DIFFRACTION100
3.2454-3.71490.22111580.192855X-RAY DIFFRACTION100
3.7149-4.680.16881070.14372943X-RAY DIFFRACTION100
4.68-53.4580.1941500.17112985X-RAY DIFFRACTION99
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)
10.4050.02170.8679-0.1138-0.02791.2621-1.08780.65570.02670.91210.61710.32540.97680.11590.00430.66480.00130.0380.37850.03730.62597.41422.672333.9808
20.12440.09940.1208-0.00190.12830.1905-0.5152-1.09120.16890.23550.58020.1467-0.11670.160300.41420.0280.00070.59-0.03460.456224.8456-4.694422.5499
30.1355-0.24080.18190.321-0.04970.12310.9355-0.2555-1.3505-0.1866-0.2422-0.05830.21450.03490.00040.4934-0.1048-0.11480.54310.08250.556434.464-8.289118.3085
40.3959-0.3565-0.22210.57180.15390.00610.0952-0.0429-0.0346-0.211-0.06890.0340.19750.5269-00.35570.0325-0.06290.52080.00870.316243.62491.373516.6996
5-0.01050.17090.2632-0.16110.30551.27850.1977-0.11130.19350.07-0.01480.3674-0.04970.0564-0.00010.29270.0052-0.0010.3718-0.02410.359734.48925.17211.2996
60.3748-0.85210.46620.6204-0.81320.2743-0.1502-0.2035-1.02070.30920.0073-0.0550.2758-0.1364-0.00010.4424-0.02420.0180.4574-0.06450.553420.8462-4.906510.3895
70.17160.0927-0.12710.02070.05780.07580.10660.52780.2134-0.08780.01490.4853-0.02970.560400.36250.0433-0.00260.4619-0.04170.441432.71019.30498.6733
80.0972-0.04470.2290.3243-0.05210.1940.04610.53670.42910.0663-0.2245-0.01420.1403-0.1976-00.3777-0.0004-0.03120.403-0.00220.40822.70637.92895.7285
9-0.0489-0.00760.2931-0.02310.133-0.2077-0.1953-0.28570.0175-0.15950.00630.1096-0.11530.0373-00.3496-0.0192-0.01440.4653-0.04180.420515.01962.74938.1452
100.1077-0.3770.19850.74880.43870.6164-0.2713-0.85430.34940.78680.08410.248-0.47780.2028-0.00010.42120.0897-0.02230.5012-0.06020.51623.238211.072618.9441
110.0567-0.174-0.04060.2954-0.04910.10770.2771-0.0220.74780.1722-0.49330.0219-0.1402-0.3791-0.00020.3484-0.08970.02720.4373-0.03710.422732.113412.312519.0682
120.4013-0.1728-0.26910.4358-1.58461.0711-0.05870.12780.14270.0048-0.01420.2137-0.20690.1039-0.00010.3189-0.0022-0.02660.3591-0.05060.340829.0572.269418.2668
130.07920.09150.04270.04380.0468-0.02940.5059-1.11761.43670.25110.3313-2.2177-1.18540.19110.00070.946-0.0828-0.09550.7131-0.01440.706454.572840.184363.0743
141.9121-0.3826-0.80540.1871-0.12990.55450.5076-0.5794-0.3435-0.57250.3168-1.19550.45090.8545-0.02880.53910.00430.1230.28280.02020.560457.520631.901151.003
150.01840.04370.04640.0562-0.07210.05871.20970.9462-0.00050.16480.04580.9348-0.8497-0.34930.00030.6967-0.0641-0.040.52730.0260.670864.73220.890737.2596
160.2455-0.2113-0.8122.5311.70713.7921-0.63512.21480.20070.3833-0.832-0.37851.5171.5196-0.10190.3547-0.1870.06540.95850.27960.633469.960516.42427.837
171.0057-0.6250.44070.41230.62850.595-0.0637-0.06780.0431-0.4405-0.4415-0.5261-0.33110.6252-1.01720.515-0.1308-0.04190.80470.19930.452161.289515.807918.0709
180.1056-0.1012-0.38471.0686-0.70950.576-0.14760.2682-0.03350.1626-0.04070.1865-0.53010.3707-00.2957-0.0276-0.02620.43640.02010.33356.274510.441626.4347
191.32941.6182-1.31890.2155-0.32051.08140.3606-0.0746-0.0741-0.1484-0.11070.038-0.07740.20380.00090.2909-0.0343-0.01870.3713-0.010.273159.2218.284434.9444
200.2592-0.42710.07350.1960.35470.5999-0.11360.09920.1468-0.4901-0.03150.07790.3869-0.03090.00010.2814-0.01750.01310.37990.02290.319852.31124.472838.1457
210.23640.3090.31210.1274-0.28430.27790.1835-0.12460.04810.1414-0.15140.0599-0.25950.2367-00.4172-0.00090.0260.3933-0.02450.35858.2796.885846.5229
22-0.02230.13230.11530.2654-0.5410.25070.3521-0.3650.7204-0.3337-0.1361-0.2496-0.5509-0.91330.00020.43120.13880.02360.50180.04260.520149.786917.966737.6124
230.1367-0.04380.14730.1890.0244-0.0341-0.18070.28670.50250.2137-0.16840.1904-0.226-0.30070.00020.48570.0217-0.09030.46840.05410.429849.472118.40228.4255
240.38780.0119-0.33020.0231-0.12150.0967-0.92031.19190.96140.77410.0758-0.5639-1.25740.5684-0.17650.7452-0.0895-0.07340.59990.29960.567358.738420.450724.0064
250.483-0.26630.50770.57370.34720.28240.19040.01950.21790.36770.1058-0.066-0.7360.8943-0.00020.4126-0.0673-0.08080.38170.03260.445459.300214.669239.8672
262.256-0.68870.63932.7834-1.1981.8508-0.4150.6090.3325-0.47060.5032-0.79210.7287-0.31940.19980.3216-0.03140.02080.5303-0.02930.135454.82592.035725.6825
270.07540.02820.06070.424-0.08260.28970.97911.3824-0.06170.39970.00940.208-0.99260.56620.00550.33160.0783-0.00290.57370.1010.506635.7802-5.863436.6418
280.1777-0.1163-0.08080.28970.21580.07060.29150.1569-0.14220.4352-0.4282-0.14360.5566-0.8321-0.00010.4982-0.0067-0.04760.5735-0.02570.66125.7298-9.003540.1774
290.655-0.0645-0.1818-0.15530.25160.36590.188-0.2281-0.0184-0.03860.12280.09590.2337-0.27380.00010.47790.0148-0.06510.61280.06240.491917.4040.874143.0649
300.7025-0.14540.678-0.13360.39190.568-0.1972-0.0761-0.0024-0.15860.2211-0.1552-0.1949-0.0267-0.00010.35480.0149-0.02310.41020.05250.340326.96423.607848.5095
311.04460.35841.31361.153-0.78673.8381-0.2311-0.10060.04290.35160.07280.41490.4179-0.1477-0.00010.2478-0.01270.01090.3673-0.04810.386634.4239-0.272749.8678
320.97880.27490.50610.6076-0.44750.289-0.1948-0.36590.54580.02350.2181-0.1169-0.0967-0.379100.41650.0013-0.02070.38530.01850.436239.04834.603253.8781
330.1811-0.24420.0261-0.0819-0.00630.5933-0.05230.19650.21960.2242-0.5112-0.16830.00230.466-0.00020.356-0.01330.03260.46910.06670.41746.4116-0.759251.2158
340.0809-0.26650.18250.6136-0.47810.3407-0.3060.26760.3022-0.95840.19740.1199-1.3120.7220.00010.4246-0.0493-0.0210.51880.12560.51538.71719.059740.9939
350.52240.44390.05050.21060.2210.59210.08220.3140.3522-0.4908-0.0774-0.0778-0.107-0.180300.38470.0821-0.040.50830.06930.419627.21887.682940.0303
360.1281-0.2144-0.0287-0.12070.3506-0.25360.0418-0.0494-0.1991-0.0802-0.3170.25690.30630.0246-0.00020.36360.0621-0.00260.41370.0540.338238.3997-0.989843.5645
370.62270.1465-0.3412-0.46-0.75680.1279-0.15760.1008-0.48830.00380.3116-0.066-0.4418-0.0836-0.00030.5227-0.08410.05210.4852-0.02120.707960.9829-30.789750.2174
380.0264-0.33830.17481.2337-0.29221.5697-0.10660.1521-0.4243-0.3395-0.0518-0.2767-0.0081-0.452900.5129-0.04350.08940.4462-0.04770.391259.8011-16.067921.4034
39-0.41631.11850.14213.3257-0.42243.2776-0.0832-0.0143-0.07880.17320.0556-0.0527-0.0768-0.1064-00.30880.0420.02650.454-0.02740.30461.2224-9.19938.5309
401.58980.8988-0.16112.39912.32612.7817-0.4689-0.1083-0.8315-0.19460.0714-0.30580.44950.4324-0.34370.39480.08060.17450.39630.09860.46566.2806-19.387832.9673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -13 through -2 )
2X-RAY DIFFRACTION2chain 'A' and (resid -1 through 3 )
3X-RAY DIFFRACTION3chain 'A' and (resid 4 through 10 )
4X-RAY DIFFRACTION4chain 'A' and (resid 11 through 24 )
5X-RAY DIFFRACTION5chain 'A' and (resid 25 through 35 )
6X-RAY DIFFRACTION6chain 'A' and (resid 36 through 47 )
7X-RAY DIFFRACTION7chain 'A' and (resid 48 through 56 )
8X-RAY DIFFRACTION8chain 'A' and (resid 57 through 67 )
9X-RAY DIFFRACTION9chain 'A' and (resid 68 through 79 )
10X-RAY DIFFRACTION10chain 'A' and (resid 80 through 90 )
11X-RAY DIFFRACTION11chain 'A' and (resid 91 through 98 )
12X-RAY DIFFRACTION12chain 'A' and (resid 99 through 112 )
13X-RAY DIFFRACTION13chain 'B' and (resid -16 through -11 )
14X-RAY DIFFRACTION14chain 'B' and (resid -10 through -2 )
15X-RAY DIFFRACTION15chain 'B' and (resid -1 through 3 )
16X-RAY DIFFRACTION16chain 'B' and (resid 4 through 10 )
17X-RAY DIFFRACTION17chain 'B' and (resid 11 through 24 )
18X-RAY DIFFRACTION18chain 'B' and (resid 25 through 35 )
19X-RAY DIFFRACTION19chain 'B' and (resid 36 through 56 )
20X-RAY DIFFRACTION20chain 'B' and (resid 57 through 67 )
21X-RAY DIFFRACTION21chain 'B' and (resid 68 through 79 )
22X-RAY DIFFRACTION22chain 'B' and (resid 80 through 90 )
23X-RAY DIFFRACTION23chain 'B' and (resid 91 through 98 )
24X-RAY DIFFRACTION24chain 'B' and (resid 99 through 104 )
25X-RAY DIFFRACTION25chain 'B' and (resid 105 through 112 )
26X-RAY DIFFRACTION26chain 'C' and (resid -14 through -2 )
27X-RAY DIFFRACTION27chain 'C' and (resid -1 through 3 )
28X-RAY DIFFRACTION28chain 'C' and (resid 4 through 10 )
29X-RAY DIFFRACTION29chain 'C' and (resid 11 through 24 )
30X-RAY DIFFRACTION30chain 'C' and (resid 25 through 35 )
31X-RAY DIFFRACTION31chain 'C' and (resid 36 through 56 )
32X-RAY DIFFRACTION32chain 'C' and (resid 57 through 67 )
33X-RAY DIFFRACTION33chain 'C' and (resid 68 through 79 )
34X-RAY DIFFRACTION34chain 'C' and (resid 80 through 90 )
35X-RAY DIFFRACTION35chain 'C' and (resid 91 through 104 )
36X-RAY DIFFRACTION36chain 'C' and (resid 105 through 112 )
37X-RAY DIFFRACTION37chain 'D' and (resid -13 through 3 )
38X-RAY DIFFRACTION38chain 'D' and (resid 4 through 35 )
39X-RAY DIFFRACTION39chain 'D' and (resid 36 through 76 )
40X-RAY DIFFRACTION40chain 'D' and (resid 77 through 112 )

+
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