[English] 日本語
Yorodumi
- PDB-5brm: Structural basis for Mob1-dependent activation of the core Mst-La... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5brm
TitleStructural basis for Mob1-dependent activation of the core Mst-Lats kinase cascade in Hippo signaling
Components
  • MOB kinase activator 1A
  • Serine/threonine-protein kinase 3Serine/threonine-specific protein kinase
KeywordsTransferase/Signaling Protein / Mst2 / Mob1 / Hippo / Transferase-Signaling Protein complex
Function / homology
Function and homology information


cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / protein localization to centrosome ...cell differentiation involved in embryonic placenta development / regulation of cell differentiation involved in embryonic placenta development / primitive hemopoiesis / neural tube formation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / endocardium development / negative regulation of organ growth / hippo signaling / Signaling by Hippo / protein localization to centrosome / organ growth / protein kinase activator activity / hepatocyte apoptotic process / regulation of MAPK cascade / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of fat cell differentiation / canonical Wnt signaling pathway / JNK cascade / protein serine/threonine kinase activator activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / epithelial cell proliferation / central nervous system development / protein tetramerization / positive regulation of JNK cascade / negative regulation of canonical Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / protein import into nucleus / negative regulation of epithelial cell proliferation / positive regulation of protein binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / apoptotic process / magnesium ion binding / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / SARAH domain / SARAH domain profile. ...: / Mst1 SARAH domain / C terminal SARAH domain of Mst1 / MOB kinase activator / MOB kinase activator family / MOB kinase activator superfamily / Mob1/phocein family / Mob1/phocein family / SARAH domain / SARAH domain profile. / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / p53-like tetramerisation domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein kinase 3 / MOB kinase activator 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å
AuthorsLuo, X. / Ni, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM085004 United States
CitationJournal: Genes Dev. / Year: 2015
Title: Structural basis for Mob1-dependent activation of the core Mst-Lats kinase cascade in Hippo signaling.
Authors: Ni, L. / Zheng, Y. / Hara, M. / Pan, D. / Luo, X.
History
DepositionMay 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Source and taxonomy
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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: MOB kinase activator 1A
B: MOB kinase activator 1A
C: MOB kinase activator 1A
D: MOB kinase activator 1A
E: MOB kinase activator 1A
F: MOB kinase activator 1A
G: Serine/threonine-protein kinase 3
H: Serine/threonine-protein kinase 3
I: Serine/threonine-protein kinase 3
J: Serine/threonine-protein kinase 3
K: Serine/threonine-protein kinase 3
L: Serine/threonine-protein kinase 3
M: Serine/threonine-protein kinase 3
N: Serine/threonine-protein kinase 3
O: Serine/threonine-protein kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,75121
Polymers158,35915
Non-polymers3926
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.188, 142.188, 135.981
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
12chain I
22chain J
32chain K
42chain L

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPZNZNchain AAA - P52 - 30113
21ASPASPZNZNchain BBB - Q52 - 30113
31ASPASPZNZNchain CCC - R52 - 30113
41ASPASPZNZNchain DDD - S52 - 30113
51ASPASPZNZNchain EEE - T52 - 30113
61ASPASPZNZNchain FFF - U52 - 30113
12TPOTPOASPASPchain III378 - 3988 - 28
22TPOTPOASPASPchain JJJ378 - 3988 - 28
32TPOTPOASPASPchain KKK378 - 3988 - 28
42TPOTPOPHEPHEchain LLL378 - 3978 - 27

NCS ensembles :
ID
1
2

-
Components

#1: Protein
MOB kinase activator 1A / Mob1 alpha / Mob1A / Mob1 homolog 1B / Mps one binder kinase activator-like 1B


Mass: 20724.754 Da / Num. of mol.: 6 / Fragment: UNP residues 41-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOB1A, C2orf6, MOB4B, MOBK1B, MOBKL1B / Plasmid: pGEX-6p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H8S9
#2: Protein/peptide
Serine/threonine-protein kinase 3 / Serine/threonine-specific protein kinase / Mammalian STE20-like protein kinase 2 / MST-2 / STE20-like kinase MST2 / Serine/threonine-protein kinase Krs-1


Mass: 3778.892 Da / Num. of mol.: 9 / Fragment: UNP residues 371-401 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q13188, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M Na Malonate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2013 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.65→40 Å / Num. obs: 46680 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 38.38 Å2 / Rmerge(I) obs: 0.091 / Χ2: 0.963 / Net I/av σ(I): 25.585 / Net I/σ(I): 11.3 / Num. measured all: 512365
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.65-2.76.311.822320.93997.9
2.7-2.748.322800.83499.9
2.74-2.89.90.96723110.85699.9
2.8-2.8510.90.89622740.883100
2.85-2.9211.60.77122930.887100
2.92-2.9811.80.71222920.891100
2.98-3.0611.90.62123040.927100
3.06-3.1411.90.46522740.95499.8
3.14-3.2311.90.34523310.96999.9
3.23-3.34120.25723000.99199.8
3.34-3.4611.80.20722941.10199.7
3.46-3.6120.14423001.00799.4
3.6-3.7611.70.11522951.07999.2
3.76-3.9611.70.09323181.04899.5
3.96-4.2111.60.07323160.98699.4
4.21-4.5311.50.06523120.96599.4
4.53-4.9811.40.06123080.97299.4
4.98-5.711.40.06323721.03199.9
5.7-7.1811.50.05723780.87499.8
7.18-4010.60.05824270.99397.8

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1pi1
Resolution: 2.651→39.295 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 27.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 2004 4.83 %random selection
Rwork0.2441 39468 --
obs0.2452 41472 89.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.2 Å2 / Biso mean: 56.5769 Å2 / Biso min: 10.42 Å2
Refinement stepCycle: final / Resolution: 2.651→39.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8906 0 6 6 8918
Biso mean--39.39 31.94 -
Num. residues----1060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069179
X-RAY DIFFRACTIONf_angle_d0.99412387
X-RAY DIFFRACTIONf_chiral_restr0.0381305
X-RAY DIFFRACTIONf_plane_restr0.0051574
X-RAY DIFFRACTIONf_dihedral_angle_d13.0393355
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6092X-RAY DIFFRACTION12.277TORSIONAL
12B6092X-RAY DIFFRACTION12.277TORSIONAL
13C6092X-RAY DIFFRACTION12.277TORSIONAL
14D6092X-RAY DIFFRACTION12.277TORSIONAL
15E6092X-RAY DIFFRACTION12.277TORSIONAL
16F6092X-RAY DIFFRACTION12.277TORSIONAL
21I283X-RAY DIFFRACTION12.277TORSIONAL
22J283X-RAY DIFFRACTION12.277TORSIONAL
23K283X-RAY DIFFRACTION12.277TORSIONAL
24L283X-RAY DIFFRACTION12.277TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.651-2.71730.3611800.30121412149246
2.7173-2.79070.2957960.30691871196760
2.7907-2.87280.3461100.30362201231171
2.8728-2.96550.33651270.30692634276183
2.9655-3.07150.31881490.30942912306194
3.0715-3.19440.341540.28663116327099
3.1944-3.33970.2771620.27731433305100
3.3397-3.51570.29031600.249731303290100
3.5157-3.73580.25641580.24033119327799
3.7358-4.0240.26471590.22983130328999
4.024-4.42840.26731580.21353146330499
4.4284-5.06810.20411640.20131633327100
5.0681-6.38080.25751580.225332163374100
6.3808-39.29930.22971690.22743275344498
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.89630.07920.10030.89530.15312.4566-0.1021-0.00080.0021-0.0107-0.03220.09970.1259-0.24350.01690.23840.0157-0.03490.2539-0.06340.04718.0532-57.4108-0.4959
26.3741.90621.56424.4660.48254.14290.06040.1327-0.1165-0.1236-0.09180.41690.104-0.45060.03250.1857-0.0316-0.10040.1996-0.13670.25231.7616-72.5646-0.9786
32.7607-0.8190.66771.2823-1.30631.3488-0.09880.58580.1912-0.4406-0.01840.4952-0.242-0.42990.05310.31350.0925-0.22320.4166-0.13920.3012-1.3222-60.5972-8.434
40.94340.17710.6110.79270.46911.6864-0.11740.02640.1035-0.047-0.10860.1528-0.0873-0.1688-0.22930.22920.003-0.05620.2558-0.1380.08148.7943-56.75833.1208
52.12290.48510.03710.40380.05051.06270.0244-0.32470.15070.1127-0.07990.0327-0.2149-0.18320.06210.3387-0.0393-0.0170.1773-0.03040.02836.0317-47.50125.5108
62.3856-0.28231.24890.6498-0.34233.3218-0.2044-0.37880.05530.1511-0.04310.1782-0.0472-0.41870.20440.4608-0.06740.08480.2149-0.080.12821.3334-54.442712.6791
70.83130.0737-0.23382.8954-0.46251.5253-0.05310.13270.0765-0.0902-0.0467-0.2501-0.00750.10720.07730.21770.08150.11560.20940.13850.146656.8243-40.3972.6172
81.9902-0.3380.22051.1316-0.33331.1166-0.203-0.3770.30410.24820.051-0.0815-0.1963-0.0782-0.0540.1831-0.0191-0.04480.36720.13540.312866.41-34.079514.3942
92.6579-0.13680.85843.96561.71754.3879-0.1527-0.5283-0.15990.80820.2533-0.68730.41750.5289-0.08490.4618-0.0623-0.03690.66940.31220.683176.7746-35.949411.5778
102.0914-0.07320.15231.67250.08430.6647-0.11550.3404-0.4658-0.2238-0.027-0.14950.25910.19210.47990.30220.12290.28640.43180.21060.556267.0003-46.7932-0.2094
110.6018-0.0559-0.00350.7147-0.03560.9579-0.0946-0.2764-0.14130.1819-0.0312-0.02960.0224-0.0271-0.14120.26120.09380.09720.23420.22010.060354.1547-41.695511.9916
121.1843-0.167-0.39510.9984-0.70192.1722-0.14220.1392-0.217-0.1702-0.126-0.1672-0.04030.0281-0.13640.2953-0.12270.15130.37830.01580.143447.8545-49.5769-4.6267
132.3805-2.10820.83973.85130.58111.17770.15650.2796-0.3576-0.1414-0.25870.36080.2596-0.07270.0730.6056-0.04330.20350.525-0.38230.765939.5935-68.7237-11.1909
149.55314.56030.21042.3237-0.92817.2-0.12140.56640.3952-0.5390.01910.0014-0.2090.17810.07490.8805-0.07010.21870.6193-0.140.516239.5361-55.9196-24.5689
155.2139-4.36964.72763.7308-4.18054.98-0.20950.12550.30750.0407-0.0455-0.2764-0.19950.0840.26351.0535-0.35010.28640.9205-0.31010.662238.6905-64.5748-21.6243
160.38970.0026-0.19010.78760.08431.3359-0.08160.2562-0.1782-0.3101-0.025-0.07560.0232-0.0573-0.02140.7315-0.13770.25190.7963-0.21670.332347.2204-56.2816-16.5137
171.2717-0.0298-0.40942.60160.29193.4114-0.12450.1349-0.0289-0.32540.121-0.1498-0.29950.55780.01440.79780.0290.15060.79340.19760.275752.0019-38.5166-15.3211
181.93250.2168-0.6750.5757-0.0632.0161-0.42480.2289-0.3893-0.19230.0844-0.08110.2777-0.17320.16660.4707-0.06650.15110.2884-0.00620.10641.1921-53.788-4.0227
196.5909-1.65050.62716.0218-0.33155.1524-0.0640.1313-0.3254-0.1869-0.06470.20230.424-0.28650.08160.1986-0.08020.06240.3892-0.07880.269530.1597-56.9161-0.9269
200.8197-0.4608-0.26850.92370.0111.3517-0.0453-0.04450.14910.032-0.0286-0.057-0.0760.20210.04780.2105-0.0258-0.03920.29620.13661.040525.507-3.3201-0.0202
215.9538-3.056-3.44367.79262.74057.92980.0238-0.00130.16980.0922-0.08450.2434-0.5088-0.38740.11590.54910.1450.1960.33470.02431.13483.9342-10.62651.8236
220.9348-0.2124-0.07390.51950.36850.2684-0.3111-0.2094-0.75050.46460.21380.3250.2949-0.06380.04880.53320.03840.30380.3749-0.02961.47046.9139-0.361110.8928
230.18370.4585-0.09891.2828-0.42010.27820.00490.06830.0447-0.1149-0.09950.0250.01550.01070.01730.34410.0376-0.08880.33160.02171.436313.26011.943-2.2992
240.85680.9415-0.25322.3878-0.60430.5615-0.0108-0.07060.44410.1738-0.12030.3275-0.0783-0.0622-0.0360.2732-0.0960.11660.3023-0.06641.193221.9633-3.68175.4709
252.41742.0584-0.51442.0772-0.77422.645-0.1225-0.25280.09250.5221-0.33560.0728-0.1189-0.0590.30750.6238-0.15350.18060.4637-0.26191.284922.0225-3.104617.8364
262.81571.5833-0.82992.3273-0.54691.468-0.06280.15960.3473-0.1522-0.1844-0.10910.00030.20550.09860.1677-0.0261-0.07310.32640.24470.567838.255-6.4281-6.6584
275.0136-3.66653.47463.3726-1.22734.90240.03220.10850.3158-0.0205-0.1988-0.7507-0.00320.80560.17050.28180.08390.07150.54580.32980.965654.2554-14.105-8.9928
283.4305-0.2051.59383.27191.98764.5451-0.270.9201-0.0872-0.68790.15760.1915-0.02610.00590.07070.8566-0.13850.17791.14860.25950.606946.8766-13.8205-22.1249
297.41051.75931.77381.06460.66141.9162-0.08440.25470.1037-0.48110.0174-0.09220.1151-0.2077-0.06510.4610.0231-0.05730.57880.37490.585636.485-8.5368-16.9971
303.1477-0.29650.52161.0320.54971.7875-0.18140.1748-0.3085-0.1505-0.10110.0860.1546-0.0417-0.24780.219-0.0645-0.07620.38370.32090.644734.6857-15.1003-10.217
312.8323-0.3196-2.50973.65910.97682.7560.2482-0.2340.25850.3966-0.18770.2176-0.22770.1246-0.07830.3877-0.1813-0.19610.4530.32480.857248.84741.16193.2183
325.4555-1.47220.69711.8725-0.45371.5305-0.0364-0.1676-0.10290.0486-0.0428-0.05130.0221-0.0245-0.01430.14930.0293-0.01630.22510.19670.591237.8638-14.58031.8167
333.3274-2.08430.79422.77810.20744.6935-0.1043-0.0577-0.30930.13860.02690.13810.19090.1270.04270.240.12560.01080.41810.19370.749647.0168-19.63792.0191
341.9973-0.0515-0.15421.9167-0.54131.5364-0.11640.41810.4439-0.4937-0.05820.2461-0.1185-0.38440.02860.55770.1182-0.14290.4710.06040.25880.5205-37.6933-10.8829
356.4585-4.68520.454.7324-0.46625.0978-0.08580.21540.5161-0.48540.06620.7073-0.8866-0.70570.010.77390.1254-0.20460.4440.29350.9188-0.0319-19.9664-12.7367
361.7569-1.29590.13781.09070.15970.60140.15120.39810.7157-0.1974-0.0041-0.052-0.8036-0.1648-0.07931.14810.0813-0.1250.73340.4320.93375.159-26.5701-25.4313
370.60810.576-0.82331.00280.1292.9231-0.0080.34190.1407-0.3748-0.06480.0469-0.0177-0.05560.05350.87050.1549-0.07870.75120.21860.30862.3114-35.4541-20.4
381.6988-1.22081.54840.9776-1.31891.83410.00890.157-0.2001-0.2397-0.0664-0.03990.44450.29580.04230.93790.04540.28080.94690.01440.357214.7156-48.7426-19.2913
392.8639-0.45090.7146.2455-1.14113.8552-0.02990.1135-0.1369-0.56620.0192-1.7262-0.03880.91330.02940.73840.06730.44480.91860.09850.828921.8003-45.1451-17.6527
400.6630.5679-0.48890.94790.4111.84150.00890.33030.5847-0.5811-0.1335-0.072-0.16510.12650.03710.59890.0991-0.03720.39540.24120.41995.7785-31.1487-10.9773
411.53880.0577-1.71581.10110.87625.11840.03450.0522-0.17450.17330.06050.34220.0063-0.2158-0.09120.42110.1745-0.06590.40420.07831.0502-12.7183-31.7036-2.6333
425.9441.1485-0.00134.4905-0.26734.07840.066-0.1460.3756-0.0902-0.2526-0.0929-0.25190.10020.09750.31810.08070.01410.17080.08640.38536.532-34.5971-1.2988
431.92590.99332.33427.7548-0.77716.711-0.02780.12840.634-0.1291-0.1467-0.1318-0.93890.60350.13670.5497-0.15870.21750.26860.03520.8316.7215-23.7188-0.6495
441.0027-0.1436-0.2021.9728-0.56061.18370.0095-0.2656-0.12550.5936-0.12110.1075-0.06910.0850.09650.33170.0538-0.0090.3463-0.01230.15359.8758-67.492916.0631
450.5993-0.986-0.56773.31413.2153.6144-0.1708-0.43060.20650.52210.3231-0.32230.03570.5754-0.15520.6017-0.1153-0.0690.5512-0.10590.167217.4135-51.730915.2501
463.06141.17741.11290.84020.06321.77350.0635-0.64370.6960.3252-0.1736-0.233-0.347-0.19790.01420.39250.00680.03140.49510.05480.295460.4545-33.200220.2357
472.5518-0.6185-1.79427.431-1.4121.73540.0731-0.68390.46930.3821-0.08190.3824-0.2713-0.39020.02940.52350.2620.0630.6270.0140.34642.4943-32.73918.6311
482.9089-2.07653.47951.4973-2.49654.18460.0756-0.2518-0.389-0.07570.32640.40790.1717-0.7798-0.41970.5729-0.02030.13780.799-0.14160.606229.3438-65.2835-9.8402
495.11931.93434.24862.30750.99483.76290.1733-0.9713-0.03021.0573-0.05670.60010.1531-0.547-0.11630.68180.06890.19550.6260.00020.72735.3232-66.40557.2967
505.4686-3.3176-4.61282.01412.80453.914-0.2566-0.3109-0.05721.22020.12760.66460.36180.02450.11660.83830.07150.16520.7714-0.2240.935210.2746-4.022918.5075
511.2138-0.25971.67183.6507-0.31462.30320.0532-0.21980.7460.165-0.0242-0.1-0.65740.1878-0.04641.14980.01540.16960.75150.02720.977118.9103-18.782618.3361
525.1649-1.2522-0.02593.06321.32992.1276-0.15-0.0723-0.01630.19540.1309-0.14860.02960.4301-0.01610.3880.15740.01470.80490.43090.643754.237-13.9849-2.9674
533.73844.6840.74466.60441.46310.53060.0186-0.29870.50930.3711-0.0183-0.5708-0.24490.3836-0.01160.74810.015-0.18210.68110.1110.948251.7854-9.177510.9301
540.2123-0.3510.11610.92360.08930.34670.18730.03680.36050.2223-0.1750.1791-0.4699-0.0364-0.08570.5804-0.0192-0.03860.75810.01581.3464-1.5064-20.9959-2.9683
550.72891.2797-0.14023.6638-2.89085.28910.12440.30860.3817-0.16840.24620.8997-0.3829-0.718-0.3160.65540.1127-0.04440.7782-0.02940.4485-4.7597-43.2155-17.1684
562.4689-0.79731.61053.625-3.71814.72170.25440.5496-0.0446-0.9702-0.1494-0.00850.1520.0826-0.04280.48180.126-0.03720.6429-0.08790.168811.3319-57.1213-11.2373
578.35267.19046.44876.40766.33617.8064-0.26780.3428-0.1494-0.59240.27480.4260.1203-0.150.00480.74050.21480.04020.7709-0.1340.596314.2121-57.4412-14.0783
580.3098-0.0746-0.13140.7078-0.10271.3904-0.05230.1249-0.0095-0.1417-0.003-0.065-0.01240.0253-0.02910.5688-0.060.18510.59780.1080.201258.173-41.7213-6.8318
591.6653-1.318-0.94841.11290.57260.9936-0.02270.1277-0.3163-0.09030.0313-0.07310.1257-0.0409-0.00750.57660.041-0.11340.34640.2430.988123.1845-3.7506-8.6407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 94 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 110 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 143 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 175 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 176 through 192 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 193 through 211 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 52 through 85 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 86 through 100 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 101 through 110 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 111 through 143 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 144 through 212 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 52 through 75 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 76 through 95 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 96 through 105 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 106 through 110 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 111 through 126 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 127 through 136 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 137 through 197 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 198 through 211 )C0
20X-RAY DIFFRACTION20chain 'D' and (resid 52 through 75 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 76 through 85 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 86 through 110 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 111 through 126 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 127 through 193 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 194 through 211 )D0
26X-RAY DIFFRACTION26chain 'E' and (resid 52 through 85 )E0
27X-RAY DIFFRACTION27chain 'E' and (resid 86 through 95 )E0
28X-RAY DIFFRACTION28chain 'E' and (resid 96 through 110 )E0
29X-RAY DIFFRACTION29chain 'E' and (resid 111 through 131 )E0
30X-RAY DIFFRACTION30chain 'E' and (resid 132 through 165 )E0
31X-RAY DIFFRACTION31chain 'E' and (resid 166 through 175 )E0
32X-RAY DIFFRACTION32chain 'E' and (resid 176 through 197 )E0
33X-RAY DIFFRACTION33chain 'E' and (resid 198 through 211 )E0
34X-RAY DIFFRACTION34chain 'F' and (resid 52 through 85 )F0
35X-RAY DIFFRACTION35chain 'F' and (resid 86 through 95 )F0
36X-RAY DIFFRACTION36chain 'F' and (resid 96 through 110 )F0
37X-RAY DIFFRACTION37chain 'F' and (resid 111 through 126 )F0
38X-RAY DIFFRACTION38chain 'F' and (resid 127 through 136 )F0
39X-RAY DIFFRACTION39chain 'F' and (resid 137 through 143 )F0
40X-RAY DIFFRACTION40chain 'F' and (resid 144 through 165 )F0
41X-RAY DIFFRACTION41chain 'F' and (resid 166 through 175 )F0
42X-RAY DIFFRACTION42chain 'F' and (resid 176 through 197 )F0
43X-RAY DIFFRACTION43chain 'F' and (resid 198 through 211 )F0
44X-RAY DIFFRACTION44chain 'G' and (resid 377 through 391 )G0
45X-RAY DIFFRACTION45chain 'G' and (resid 392 through 398 )G0
46X-RAY DIFFRACTION46chain 'H' and (resid 377 through 393 )H0
47X-RAY DIFFRACTION47chain 'H' and (resid 394 through 399 )H0
48X-RAY DIFFRACTION48chain 'I' and (resid 379 through 392 )I0
49X-RAY DIFFRACTION49chain 'I' and (resid 393 through 398 )I0
50X-RAY DIFFRACTION50chain 'J' and (resid 379 through 393 )J0
51X-RAY DIFFRACTION51chain 'J' and (resid 394 through 398 )J0
52X-RAY DIFFRACTION52chain 'K' and (resid 379 through 393 )K0
53X-RAY DIFFRACTION53chain 'K' and (resid 394 through 398 )K0
54X-RAY DIFFRACTION54chain 'L' and (resid 379 through 397 )L0
55X-RAY DIFFRACTION55chain 'M' and (resid 380 through 389 )M0
56X-RAY DIFFRACTION56chain 'M' and (resid 390 through 394 )M0
57X-RAY DIFFRACTION57chain 'M' and (resid 395 through 396 )M0
58X-RAY DIFFRACTION58chain 'N' and (resid 385 through 396 )N0
59X-RAY DIFFRACTION59chain 'O' and (resid 386 through 393 )O0

+
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