[English] 日本語
Yorodumi
- PDB-8gi4: Crystal structure of human LIMK2 PDZ domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gi4
TitleCrystal structure of human LIMK2 PDZ domain
ComponentsLIM domain kinase 2
KeywordsSIGNALING PROTEIN / PDZ domain / protein kinase / autoregulation / cofilin
Function / homology
Function and homology information


cornea development in camera-type eye / establishment of vesicle localization / head development / astral microtubule organization / negative regulation of cilium assembly / cis-Golgi network / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / phosphorylation / EPHB-mediated forward signaling ...cornea development in camera-type eye / establishment of vesicle localization / head development / astral microtubule organization / negative regulation of cilium assembly / cis-Golgi network / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / phosphorylation / EPHB-mediated forward signaling / mitotic spindle / positive regulation of protein localization to nucleus / actin cytoskeleton organization / spermatogenesis / non-specific serine/threonine protein kinase / positive regulation of protein phosphorylation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...: / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsCasanova Sepulveda, G. / Boggon, T.J.
Funding support United States, 3items
OrganizationGrant numberCountry
American Heart Association835293 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102262 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM138411 United States
CitationJournal: Nat Commun / Year: 2023
Title: Autoregulation of the LIM kinases by their PDZ domain.
Authors: Casanova-Sepulveda, G. / Sexton, J.A. / Turk, B.E. / Boggon, T.J.
History
DepositionMar 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LIM domain kinase 2
B: LIM domain kinase 2
C: LIM domain kinase 2
D: LIM domain kinase 2
E: LIM domain kinase 2
F: LIM domain kinase 2
G: LIM domain kinase 2
H: LIM domain kinase 2


Theoretical massNumber of molelcules
Total (without water)109,8348
Polymers109,8348
Non-polymers00
Water4,125229
1
A: LIM domain kinase 2


Theoretical massNumber of molelcules
Total (without water)13,7291
Polymers13,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIM domain kinase 2


Theoretical massNumber of molelcules
Total (without water)13,7291
Polymers13,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: LIM domain kinase 2


Theoretical massNumber of molelcules
Total (without water)13,7291
Polymers13,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: LIM domain kinase 2


Theoretical massNumber of molelcules
Total (without water)13,7291
Polymers13,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: LIM domain kinase 2


Theoretical massNumber of molelcules
Total (without water)13,7291
Polymers13,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: LIM domain kinase 2


Theoretical massNumber of molelcules
Total (without water)13,7291
Polymers13,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: LIM domain kinase 2


Theoretical massNumber of molelcules
Total (without water)13,7291
Polymers13,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: LIM domain kinase 2


Theoretical massNumber of molelcules
Total (without water)13,7291
Polymers13,7291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.950, 83.028, 83.080
Angle α, β, γ (deg.)90.00, 96.58, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
LIM domain kinase 2 / LIMK-2


Mass: 13729.308 Da / Num. of mol.: 8 / Fragment: PDZ domain (UNP residues 130-250) / Mutation: C173S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMK2 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P53671, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 10% 2-propanol, 20% PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→83.13 Å / Num. obs: 68051 / % possible obs: 98.3 % / Redundancy: 19.5 % / CC1/2: 0.996 / Rpim(I) all: 0.033 / Rrim(I) all: 0.146 / Net I/σ(I): 23.1 / Num. measured all: 1329519
Reflection shellResolution: 2.05→2.16 Å / % possible obs: 88.5 % / Redundancy: 14.4 % / Num. measured all: 127846 / Num. unique obs: 8868 / CC1/2: 0.517 / Rpim(I) all: 0.44 / Rrim(I) all: 1.706 / Net I/σ(I) obs: 1.9

-
Processing

Software
NameVersionClassification
PHENIXv2.8.3refinement
SCALAdata scaling
PHASERv2.8.3phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→80.42 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 3197 4.73 %
Rwork0.209 --
obs0.2102 67544 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→80.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5822 0 0 229 6051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025950
X-RAY DIFFRACTIONf_angle_d0.458102
X-RAY DIFFRACTIONf_dihedral_angle_d13.5342250
X-RAY DIFFRACTIONf_chiral_restr0.044978
X-RAY DIFFRACTIONf_plane_restr0.0031070
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.090.35931300.37282682X-RAY DIFFRACTION96
2.09-2.120.38261100.35322826X-RAY DIFFRACTION100
2.12-2.160.34941150.33792778X-RAY DIFFRACTION100
2.16-2.20.31571310.29582817X-RAY DIFFRACTION100
2.2-2.240.35351160.28092814X-RAY DIFFRACTION100
2.24-2.280.34131270.28582779X-RAY DIFFRACTION100
2.28-2.320.27611440.26522805X-RAY DIFFRACTION100
2.32-2.380.27881310.26282812X-RAY DIFFRACTION100
2.38-2.430.29191440.25282756X-RAY DIFFRACTION100
2.43-2.490.29231500.26742768X-RAY DIFFRACTION100
2.49-2.560.29921530.2562775X-RAY DIFFRACTION100
2.56-2.630.27721440.25762794X-RAY DIFFRACTION100
2.63-2.720.2981330.26622823X-RAY DIFFRACTION100
2.72-2.820.27771640.25492758X-RAY DIFFRACTION100
2.82-2.930.30451530.24772779X-RAY DIFFRACTION100
2.93-3.060.27951570.24072799X-RAY DIFFRACTION100
3.06-3.220.25651270.22462831X-RAY DIFFRACTION100
3.22-3.430.27141270.23142806X-RAY DIFFRACTION100
3.43-3.690.21691470.20122814X-RAY DIFFRACTION100
3.69-4.060.20011390.1732807X-RAY DIFFRACTION100
4.06-4.650.1731220.14752847X-RAY DIFFRACTION100
4.65-5.860.22271330.17322843X-RAY DIFFRACTION100
5.86-80.420.18472000.17542834X-RAY DIFFRACTION100
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)
13.24263.0644-2.14438.3563-1.93355.1162-0.35870.3888-0.8005-0.5669-0.1672-0.56620.5381-0.17050.45270.6503-0.01460.04660.3770.01580.3564-0.43869.502-27.3352
26.80372.8497-0.94538.42161.82434.3519-0.08690.4712-0.7007-0.08910.0515-0.68320.62950.4478-0.05270.53570.0230.11470.3390.01880.45043.62315.6042-23.8602
35.45345.92235.36817.00664.73337.08160.6914-1.058-0.73141.0877-0.6098-0.01610.9229-0.8565-0.08040.7289-0.0840.10790.44070.0190.4143-1.47118.2012-14.0224
43.35035.6119-1.93239.7447-2.692810.2279-0.15980.2964-1.2482-0.6315-0.4667-1.15890.57330.80810.65860.6664-0.00810.07060.47780.01220.5025.171812.3168-26.846
51.9385-0.5939-2.01885.76283.03244.5951-0.2485-0.1265-0.35080.34860.11510.09910.15780.07530.02150.569-0.00570.01530.4169-0.01260.4179-31.199615.5553-13.9695
63.2486-0.50681.27232.32020.96772.22210.31940.2126-0.4597-1.29910.5421.54640.7532-1.067-0.73240.9115-0.0312-0.04540.56910.06520.6685-38.168418.4231-30.4795
73.9444-3.66532.42134.8373-0.35984.0876-0.136-0.2255-0.9215-1.41280.92211.76562.3309-1.3132-0.81730.5667-0.08640.01920.46550.05560.5002-37.433411.7311-21.9993
87.797-6.8873.64659.0165-4.38398.5865-0.8166-1.4086-0.39551.48740.90050.3503-0.4241-0.39770.08510.7450.07340.08140.62820.07330.4919-32.36939.7025-10.728
97.1416.5929-5.43886.2591-4.52518.9625-0.9051-0.681.8325-1.11750.3611.3841-1.5644-0.49360.38760.90850.06080.02970.3938-0.08450.5781-34.011421.77-20.8605
109.88383.44370.6557.3495.02283.84560.6424-0.6109-0.1015-0.1353-0.0358-0.6914-0.85150.1197-0.59320.6208-0.00410.01050.32460.00550.4204-29.661424.5903-27.3063
118.0174-4.33473.62995.7456-5.40166.14460.41110.8412-0.2518-1.694-0.2762-1.33621.42291.967-0.34110.82770.04470.0160.4221-0.10990.5995-26.80714.9267-28.9979
126.52264.14745.59345.34495.35785.98670.86472.07612.9676-2.0362-0.5518-2.4228-1.18430.9826-0.21850.70670.13190.18590.5791-0.01421.0738-18.737813.0835-20.8676
135.7917-3.8737-3.67567.46861.19694.0807-0.2362-1.59860.34361.40090.18340.0451-1.0695-0.61510.19830.77360.1431-0.00620.4377-0.01760.4664-32.625420.1408-15.9844
143.671-3.33655.69784.0551-5.66269.6488-0.8022-1.06370.241610.78030.4101-0.9396-1.281-0.04330.67360.05180.01620.49280.07870.5405-38.06033.0309-47.8496
154.1635-3.6947-1.87697.52090.19233.8412-0.7648-1.79021.12031.28770.4583-0.6588-0.67740.3880.14770.6410.0738-0.13660.4697-0.07240.4014-26.216-3.9929-32.3935
168.36910.05263.76599.52324.36653.94090.9186-0.3645-1.1260.5634-0.7641.7042.0966-1.5369-0.38440.9971-0.10410.04880.89010.25030.774-44.4195-14.7868-38.6062
177.68272.28825.4778.88872.82228.3423-0.3224-1.3121.33041.1202-0.18020.1033-0.4611-0.15860.39450.66410.1573-0.03070.4098-0.00440.5773-32.69821.801-35.029
189.0121-0.27821.46112.56171.26167.8164-0.5490.40320.54670.73820.2721-0.1632-1.1225-0.46630.26170.74780.1355-0.0690.388-0.0060.642-35.26424.9469-38.5326
197.16824.0489-1.30468.1170.52036.16220.1536-0.2258-0.54270.34990.226-0.83550.5863-0.1457-0.2830.5871-0.0025-0.05430.26630.06160.4343-37.4018-11.3739-45.0735
205.15364.04265.05083.54353.57056.4911.3205-1.644-1.52151.7325-0.5901-0.18951.5752-1.4471-0.66810.8353-0.0395-0.03090.56090.14510.4936-33.7843-14.0936-35.8284
213.5241-1.66253.58917.48033.34727.8299-0.16140.3348-2.00451.0162-0.3645-0.36113.71181.2699-0.04430.71720.0995-0.12790.476-0.01240.6739-23.0279-10.1465-36.927
225.3198-6.74455.52310.0198-7.06985.8477-0.1006-0.81540.32460.07960.6360.911-0.4179-0.9069-0.57670.73220.09010.02150.42180.0070.5709-37.3426-0.0191-44.559
2310.00987.5507-6.08539.9546-5.77269.6159-0.30840.9276-0.0249-0.76590.80160.4820.797-1.2313-0.39170.75660.01220.09190.44480.08350.474-44.4075-15.93455.9231
249.42633.64157.15195.7297-0.07658.2176-0.8040.7278-0.6511-0.99330.365-0.5146-0.20080.62410.4390.6786-0.0110.15940.4403-0.12430.4375-29.5305-8.7994-6.7424
259.3206-2.9663-3.2569.47242.78494.62080.23230.8938-0.3134-1.3777-0.09380.0241-0.1296-0.6251-0.13550.6751-0.09240.02120.53480.02850.3537-41.2274-8.1575-5.131
269.6982-5.8999-1.18616.3971.09292.8482-0.9336-0.0295-1.6277-0.18590.5518-0.31760.8393-0.42820.63550.9819-0.12460.16390.4187-0.10730.758-39.561-17.8614-2.659
273.93724.56833.11965.25033.64313.0718-0.31620.03170.8561-0.64570.51-0.0323-1.235-1.149-0.10960.61820.0250.04570.42580.04020.5193-43.8502-6.62222.7292
289.6179-6.64-4.6046.96083.24354.11460.71760.76251.0396-0.5843-0.4702-0.5118-0.8714-0.1579-0.23420.75040.03570.0930.34580.0510.4892-37.52240.5852-0.8811
299.83116.9275-1.92165.1146-1.57593.73850.1722-0.26940.0581.00170.03610.581-0.0544-0.1534-0.26570.67840.06870.20310.3484-0.03370.5616-41.3048-11.70883.4368
304.9371-4.2795-4.43899.04113.80064.1203-0.7355-0.44150.41410.71540.6366-0.41250.38290.90750.21150.7073-0.0280.07370.6252-0.06390.3714.2667-20.7135-49.1443
313.22071.7642.27183.6828-0.63622.8388-0.8944-0.4962-0.18810.3370.023-0.3972-1.0543-0.90490.54070.66250.01740.09250.6530.01770.5397-11.8509-12.8339-35.673
327.1392.4778-2.72314.4651-0.40684.1610.1533-0.2538-0.01191.0415-0.7671-1.6574-1.5791.23220.47420.7173-0.11440.0030.45250.02220.43525.4228-4.5736-42.9805
338.876-0.6833-5.11267.0555-2.36114.0861-1.0741-0.3201-1.4190.58850.16180.55782.0201-0.00940.73470.70350.00780.13220.46720.06630.5457-6.0446-21.3236-35.736
344.23326.0833-2.61259.2604-2.06378.955-0.5475-0.3723-2.60070.44720.0132-0.58521.6086-0.06970.48740.67840.03770.14680.45180.02340.75821.7629-19.799-39.6054
354.522-3.30285.41114.3515-2.77917.3309-0.06751.43330.4014-1.87660.1397-0.5584-1.54371.83220.05810.874-0.11260.18350.5193-0.0390.41751.5261-10.6953-49.243
366.34355.0896-1.29578.6756-3.19161.32310.35840.0027-0.1789-0.91-0.1128-0.0492-0.704-0.1551-0.25740.8096-0.04150.07970.3887-0.0140.3801-1.7807-3.8773-52.327
377.26692.8256-4.43434.1137-5.26598.45060.7649-0.79430.95492.0919-0.53811.8011-1.6591-0.7582-0.22240.7282-0.05450.13610.479-0.12290.4389-5.4767-1.9577-42.9921
386.40970.8336-4.52039.02890.27255.16571.05261.69832.4763-1.3481-0.24320.4235-2.3731-1.8449-1.04460.67680.19210.14940.80560.07280.5103-14.4929-8.9384-42.1507
395.3612-1.379-5.30118.2858-0.08915.58630.0123-0.2446-1.069-0.3969-0.0608-0.59030.46910.5835-0.10840.66560.00270.10770.4908-0.03990.5320.9606-15.8647-47.6172
407.7726.37614.24719.71814.46444.2483-0.0907-0.55271.09190.0087-0.43951.0986-0.3308-0.67420.59410.6153-0.05210.03340.4078-0.07540.4278-35.7172-34.9717-29.7054
418.53860.09580.89232.2085-2.58122.9153-0.3396-0.53870.48930.96440.530.2078-1.4015-0.56550.09860.64050.047-0.06350.4131-0.00450.596-21.8395-19.8665-20.3229
429.8915.4252-4.94144.5386-1.01065.52120.3794-0.49791.26190.4407-0.09731.6818-0.9223-1.7062-1.09810.72470.09240.12560.47370.0340.4836-36.1106-25.3037-15.3479
436.1183.7164-3.65215.5448-5.53085.90330.2603-0.04140.43190.90330.64351.7738-0.5354-1.0794-0.71090.66840.02370.13630.5316-0.02070.6006-40.4551-30.3803-13.1778
446.20384.6452-0.19874.9082-3.919.6498-0.95210.98560.3811-1.07670.497-1.18090.170.72840.07930.8555-0.0865-0.0260.46690.03410.5143-26.7166-20.5775-29.3922
459.25323.1332-6.8117.2482-1.95876.2888-0.56641.49820.3256-1.73770.51750.0721-0.3018-0.99810.12760.721-0.0682-0.06080.6267-0.05490.5559-34.2529-25.118-28.6357
466.3228-4.94834.16547.7008-3.21244.8811-0.1232-0.3358-2.28131.76740.24481.4851.7232-0.14290.14480.7532-0.06120.13770.3004-0.10740.5124-34.0301-34.715-19.474
477.2811-0.15861.21732.6818-0.24072.35140.41160.47910.210.9228-0.2427-0.61771.4625-0.1405-0.02180.7114-0.05780.07780.3167-0.02780.4869-31.1887-37.4748-12.2213
487.8934.9801-3.99514.0838-3.94894.18680.5611-0.4970.3191.6686-0.2769-0.0504-1.60560.7788-0.08060.7211-0.03540.03560.3892-0.07420.525-28.7972-27.861-9.892
495.0326.3210.80259.35590.43617.1268-0.13140.4107-0.22590.83340.1284-0.435-0.01230.3953-0.11480.65460.0085-0.00080.2765-0.01740.4921-26.6685-30.2964-20.8793
502.93611.99343.32734.57644.14577.563-0.32650.6546-0.1536-0.46940.4001-0.0797-0.12210.47730.08340.6424-0.00510.06670.4503-0.03450.3632-7.7834-5.49080.4323
512.8356-0.26340.10719.329-4.16828.3485-0.1756-0.00740.1136-0.05410.001-0.40160.04830.10870.19980.5384-0.02530.03590.3638-0.08250.3001-5.9724-12.83881.2254
522.1611-3.91762.0858.181-4.33783.4333-0.5773-0.43690.63940.67320.0958-1.1091-0.8091-0.15110.25570.80450.0661-0.00740.46770.06210.52934.4239-38.4802-10.8883
538.08894.21460.72569.1537-0.77157.4109-0.4703-0.2290.7693-0.01680.54110.7008-1.2695-0.60660.09650.64560.1142-0.01860.3817-0.06540.4733-10.0007-24.1033-19.8672
549.53523.5096-4.19062.0883-2.29269.6656-0.5605-1.11020.24470.1903-0.3552-1.74-0.31651.40420.72770.77330.0131-0.01950.47010.09370.74566.1653-25.2832-20.5667
559.0025-2.72750.82946.45821.15355.67781.16920.65081.4926-1.28820.2875-1.7804-1.44970.5218-0.60480.8226-0.12810.10270.42840.15870.7889.6961-27.881-23.764
563.06-2.5703-0.75663.60212.6893.0017-0.666-1.10790.48021.19970.27050.5583-1.2739-1.07950.28890.83680.21050.00770.69030.0120.5144-7.9633-26.9232-10.0501
572.1075-2.4841-2.92834.1462.35074.7184-0.0482-1.6177-0.07930.470.1205-0.0154-0.4997-0.1401-0.01590.82120.0936-0.03390.61810.02120.39380.4088-29.5274-9.3778
588.4674-2.373-1.41085.2064-0.47585.59940.06920.551-0.0479-0.7323-0.3484-0.2536-0.4911-0.05620.1470.65340.04040.1030.36370.04470.33625.2342-35.7308-25.321
594.596-5.9782-2.93679.64221.79457.26161.01730.59951.5323-1.0387-0.5761-1.3086-1.2934-0.0145-0.34740.91660.05060.11550.42450.09320.59851.1639-26.922-28.4894
609.7976-5.30555.24526.652-2.09479.35740.35790.58910.1603-0.2202-0.4024-0.04320.47460.08390.17360.59480.06120.12630.330.02130.3505-2.1892-33.3159-19.1428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 145 through 164 )
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 207 )
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 230 )
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 239 )
5X-RAY DIFFRACTION5chain 'B' and (resid 145 through 164 )
6X-RAY DIFFRACTION6chain 'B' and (resid 165 through 178 )
7X-RAY DIFFRACTION7chain 'B' and (resid 179 through 185 )
8X-RAY DIFFRACTION8chain 'B' and (resid 186 through 202 )
9X-RAY DIFFRACTION9chain 'B' and (resid 203 through 207 )
10X-RAY DIFFRACTION10chain 'B' and (resid 208 through 216 )
11X-RAY DIFFRACTION11chain 'B' and (resid 217 through 225 )
12X-RAY DIFFRACTION12chain 'B' and (resid 226 through 230 )
13X-RAY DIFFRACTION13chain 'B' and (resid 231 through 237 )
14X-RAY DIFFRACTION14chain 'C' and (resid 145 through 155 )
15X-RAY DIFFRACTION15chain 'C' and (resid 156 through 166 )
16X-RAY DIFFRACTION16chain 'C' and (resid 167 through 178 )
17X-RAY DIFFRACTION17chain 'C' and (resid 179 through 194 )
18X-RAY DIFFRACTION18chain 'C' and (resid 195 through 202 )
19X-RAY DIFFRACTION19chain 'C' and (resid 203 through 216 )
20X-RAY DIFFRACTION20chain 'C' and (resid 217 through 225 )
21X-RAY DIFFRACTION21chain 'C' and (resid 226 through 230 )
22X-RAY DIFFRACTION22chain 'C' and (resid 231 through 239 )
23X-RAY DIFFRACTION23chain 'D' and (resid 145 through 155 )
24X-RAY DIFFRACTION24chain 'D' and (resid 156 through 166 )
25X-RAY DIFFRACTION25chain 'D' and (resid 167 through 194 )
26X-RAY DIFFRACTION26chain 'D' and (resid 195 through 202 )
27X-RAY DIFFRACTION27chain 'D' and (resid 203 through 207 )
28X-RAY DIFFRACTION28chain 'D' and (resid 208 through 230 )
29X-RAY DIFFRACTION29chain 'D' and (resid 231 through 237 )
30X-RAY DIFFRACTION30chain 'E' and (resid 145 through 155 )
31X-RAY DIFFRACTION31chain 'E' and (resid 156 through 164 )
32X-RAY DIFFRACTION32chain 'E' and (resid 165 through 185 )
33X-RAY DIFFRACTION33chain 'E' and (resid 186 through 194 )
34X-RAY DIFFRACTION34chain 'E' and (resid 195 through 202 )
35X-RAY DIFFRACTION35chain 'E' and (resid 203 through 207 )
36X-RAY DIFFRACTION36chain 'E' and (resid 208 through 216 )
37X-RAY DIFFRACTION37chain 'E' and (resid 217 through 225 )
38X-RAY DIFFRACTION38chain 'E' and (resid 226 through 230 )
39X-RAY DIFFRACTION39chain 'E' and (resid 231 through 238 )
40X-RAY DIFFRACTION40chain 'F' and (resid 145 through 155 )
41X-RAY DIFFRACTION41chain 'F' and (resid 156 through 164 )
42X-RAY DIFFRACTION42chain 'F' and (resid 165 through 170 )
43X-RAY DIFFRACTION43chain 'F' and (resid 171 through 185 )
44X-RAY DIFFRACTION44chain 'F' and (resid 186 through 194 )
45X-RAY DIFFRACTION45chain 'F' and (resid 195 through 202 )
46X-RAY DIFFRACTION46chain 'F' and (resid 203 through 207 )
47X-RAY DIFFRACTION47chain 'F' and (resid 208 through 216 )
48X-RAY DIFFRACTION48chain 'F' and (resid 217 through 225 )
49X-RAY DIFFRACTION49chain 'F' and (resid 226 through 237 )
50X-RAY DIFFRACTION50chain 'G' and (resid 145 through 164 )
51X-RAY DIFFRACTION51chain 'G' and (resid 165 through 238 )
52X-RAY DIFFRACTION52chain 'H' and (resid 145 through 155 )
53X-RAY DIFFRACTION53chain 'H' and (resid 156 through 164 )
54X-RAY DIFFRACTION54chain 'H' and (resid 165 through 170 )
55X-RAY DIFFRACTION55chain 'H' and (resid 171 through 185 )
56X-RAY DIFFRACTION56chain 'H' and (resid 186 through 194 )
57X-RAY DIFFRACTION57chain 'H' and (resid 195 through 202 )
58X-RAY DIFFRACTION58chain 'H' and (resid 203 through 216 )
59X-RAY DIFFRACTION59chain 'H' and (resid 217 through 225 )
60X-RAY DIFFRACTION60chain 'H' and (resid 226 through 237 )

+
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