[English] 日本語
Yorodumi
- PDB-3gjx: Crystal Structure of the Nuclear Export Complex CRM1-Snurportin1-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gjx
TitleCrystal Structure of the Nuclear Export Complex CRM1-Snurportin1-RanGTP
Components
  • Exportin-1
  • GTP-binding nuclear protein Ran
  • Snurportin-1
KeywordsPROTEIN TRANSPORT / Transport / Cytoplasm / Nucleus / RNA-binding / Acetylation / GTP-binding / Host-virus interaction / Nucleotide-binding / Phosphoprotein / Polymorphism / mRNA transport
Function / homology
Function and homology information


Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Cyclin A/B1/B2 associated events during G2/M transition / Heme signaling / HuR (ELAVL1) binds and stabilizes mRNA / RNA import into nucleus / Transcriptional and post-translational regulation of MITF-M expression and activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deactivation of the beta-catenin transactivating complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation ...Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Cyclin A/B1/B2 associated events during G2/M transition / Heme signaling / HuR (ELAVL1) binds and stabilizes mRNA / RNA import into nucleus / Transcriptional and post-translational regulation of MITF-M expression and activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Deactivation of the beta-catenin transactivating complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / RHO GTPases Activate Formins / Separation of Sister Chromatids / RNA cap binding / regulation of centrosome duplication / RNA nuclear export complex / MAPK6/MAPK4 signaling / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / regulation of protein export from nucleus / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / GTP metabolic process / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / nuclear import signal receptor activity / DNA metabolic process / dynein intermediate chain binding / regulation of protein catabolic process / mitotic sister chromatid segregation / protein localization to nucleus / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / ribosomal subunit export from nucleus / mRNA export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / Cajal body / centriole / viral process / protein export from nucleus / mitotic spindle organization / G protein activity / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / recycling endosome / kinetochore / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / snRNP Assembly / midbody / actin cytoskeleton organization / nuclear membrane / DNA-binding transcription factor binding / ribonucleoprotein complex / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / DNA ligase/mRNA capping enzyme / Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal ...Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / DNA ligase/mRNA capping enzyme / Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / D-amino Acid Aminotransferase; Chain A, domain 1 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Alpha Horseshoe / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Snurportin-1 / GTP-binding nuclear protein Ran / Exportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMonecke, T. / Guettler, T. / Neumann, P. / Dickmanns, A. / Goerlich, D. / Ficner, R.
CitationJournal: Science / Year: 2009
Title: Crystal Structure of the Nuclear Export Receptor CRM1 in Complex with Snurportin1 and RanGTP.
Authors: Monecke, T. / Guttler, T. / Neumann, P. / Dickmanns, A. / Gorlich, D. / Ficner, R.
History
DepositionMar 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Snurportin-1
C: GTP-binding nuclear protein Ran
A: Exportin-1
E: Snurportin-1
F: GTP-binding nuclear protein Ran
D: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,01513
Polymers378,8396
Non-polymers1,1767
Water17,276959
1
B: Snurportin-1
C: GTP-binding nuclear protein Ran
A: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,9906
Polymers189,4193
Non-polymers5703
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-62 kcal/mol
Surface area65050 Å2
MethodPISA
2
E: Snurportin-1
F: GTP-binding nuclear protein Ran
D: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,0257
Polymers189,4193
Non-polymers6064
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-73 kcal/mol
Surface area63980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.173, 225.738, 163.451
Angle α, β, γ (deg.)90.00, 100.56, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 3 types, 6 molecules BECFAD

#1: Protein Snurportin-1 / RNA U transporter 1


Mass: 41610.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNUPN, RNUT1, SPN1 / Production host: Escherichia coli (E. coli) / References: UniProt: O95149
#2: Protein GTP-binding nuclear protein Ran / RanGTP / GTPase Ran / Ras-related nuclear protein / Ras-like protein TC4 / Androgen receptor- ...RanGTP / GTPase Ran / Ras-related nuclear protein / Ras-like protein TC4 / Androgen receptor-associated protein 24


Mass: 24441.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Production host: Escherichia coli (E. coli) / References: UniProt: P62826
#3: Protein Exportin-1 / Crm1 / Exp1 / Chromosome region maintenance 1 protein homolog


Mass: 123367.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Xpo1, Crm1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6P5F9

-
Non-polymers , 5 types, 966 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 959 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews3/Da)Density % sol (%)
13.4664.4
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop8PEG 1000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting drop8PEG 1000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.110.9
SYNCHROTRONBESSY 14.120.9
Detector
TypeIDDetectorDateDetails
MARMOSAIC 225 mm CCD1CCDDec 19, 2007mirrors
MARMOSAIC 225 mm CCD2CCDDec 20, 2007mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→39.56 Å / Num. all: 176505 / Num. obs: 176505 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 38.453 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.124 / Net I/σ(I): 10.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.9 / Num. measured obs: 75431 / Num. unique all: 19500 / Num. unique obs: 19500 / Rsym value: 0.5 / % possible all: 99.7

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→38.842 Å / Cor.coef. Fo:Fc: 0.831 / Cor.coef. Fo:Fc free: 0.811 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.389 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 0 / ESU R: 0.416 / ESU R Free: 0.295 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2808 8604 5 %RANDOM
Rwork0.2443 ---
all0.31 176504 --
obs0.2461 172082 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.356 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso max: 131.5 Å2 / Biso mean: 50.035 Å2 / Biso min: 12.34 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24252 0 69 959 25280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724872
X-RAY DIFFRACTIONf_angle_d1.07933732
X-RAY DIFFRACTIONf_dihedral_angle_d18.6259152
X-RAY DIFFRACTIONf_chiral_restr0.0843781
X-RAY DIFFRACTIONf_plane_restr0.0054303
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.52840.32942790.2811528396
2.5284-2.55820.34612830.2721539096
2.5582-2.58930.30522840.2598539197
2.5893-2.62210.29722830.2542537497
2.6221-2.65660.32052900.2512550498
2.6566-2.6930.32672870.2537546698
2.693-2.73150.31582890.2663548098
2.7315-2.77220.31772910.2592553198
2.7722-2.81550.31232890.25548699
2.8155-2.86170.30122890.2496549698
2.8617-2.9110.2822900.2444551698
2.911-2.96390.30792880.2534546899
2.9639-3.02090.29032910.2456553998
3.0209-3.08250.32052880.2514545898
3.0825-3.14950.29422900.2455551798
3.1495-3.22280.2982870.2482545198
3.2228-3.30330.27422900.2383550898
3.3033-3.39260.27342880.2299547498
3.3926-3.49240.24212860.2252542698
3.4924-3.6050.2622900.2253551598
3.605-3.73370.27352850.2286542197
3.7337-3.88310.2552890.2215547897
3.8831-4.05970.2722860.2326545197
4.0597-4.27340.26912880.2321545897
4.2734-4.54080.25652860.2195543997
4.5408-4.89080.22972850.2179541397
4.8908-5.38180.27772850.2373541297
5.3818-6.15790.26272840.2576539596
6.1579-7.74820.27952830.2574539396
7.7482-38.8470.24382810.242534594
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)
10.0043-0.0671-0.0275-0.0776-0.041-0.0382-0.06960.03060.1128-0.01350.0072-0.0727-0.0407-0.12750.01640.0512-0.0184-0.01240.2612-0.09170.507254.4371-62.9557-2.968
20.34330.21340.14550.34520.04930.3676-0.03030.01780.45830.00010.06750.2077-0.0780.0530.01160.0780.0107-0.01330.1423-0.01290.52527.9503-61.8833-4.9291
30.0002-0.0031-0.0090.0074-0.0013-0.0028-0.0839-0.0714-0.0683-0.0005-0.0575-0.080.04990.0112-0.00030.4256-0.01960.0510.72250.03550.810127.1606-105.44625.435
40.02680.0185-0.0359-0.07840.04930.0621-0.04030.1174-0.4378-0.1203-0.12390.03130.2153-0.14420.0860.08960.0114-0.02220.1606-0.1060.635818.8146-150.5642-1.8724
50.5939-0.00920.32710.27610.1040.30540.0251-0.0138-0.57220.03130.10410.30510.03710.0474-0.15760.06140.01760.02340.1113-0.00390.6103-8.0332-151.9906-0.3197
60.08560.0199-0.3004-0.02160.0174-0.0406-0.05620.08380.0580.0241-0.024-0.0475-0.09040.00220.00650.7077-0.01120.08170.820.12580.4252-8.6453-109.7659-9.8881
7-0.0284-0.01490.12450.037-0.02270.15440.06650.25370.1564-0.21010.10820.0484-0.0299-0.08560.4981-0.089-0.027-0.36770.3034-0.0477-0.297841.4046-93.4266-46.0937
80.3671-0.1907-0.00610.57690.24360.21710.0584-0.29530.12740.2392-0.0022-0.21020.0367-0.0570.03050.11240.02480.06060.30780.0045-0.02155.4178-120.268640.6535
90.01040.0056-0.01790.0453-0.01940.0173-0.07130.0198-0.0179-0.00950.0489-0.08270.05440.06440.00950.6269-0.0928-0.0640.7535-0.1270.354160.218-132.5771-48.1303
100.0922-0.02310.03240.06430.09660.0708-0.05420.2145-0.0767-0.0275-0.0012-0.08590.4871-0.05790.04080.3291-0.04980.03330.4047-0.28070.33147.6864-130.65-47.2037
110.0264-0.02730.00670.0483-0.06550.1637-0.0155-0.0162-0.09440.01350.01870.03960.10390.3573-0.03140.25220.0630.13710.2001-0.24110.220844.4386-130.7432-33.7104
120.1820.0781-0.04930.21380.05580.0684-0.0250.0944-0.11860.03010.0040.1235-0.04940.0324-0.00890.0535-0.0001-0.03550.1043-0.06620.229935.0861-116.0507-19.0776
130.09380.1244-0.0454-0.04640.16630.09920.02750.0019-0.0813-0.0032-0.0118-0.00720.0265-0.006-0.01930.0861-0.0118-0.02990.0897-0.01190.31132.8794-94.1762-6.1132
140.16460.28630.06120.20790.07160.2872-0.11610.0990.220.0152-0.03490.06440.079-0.13270.10570.10120.00540.00780.15130.00410.355753.6883-77.6129-6.8861
15-0.04290.16420.02110.02460.08740.16230.06020.01110.067-0.06760.0943-0.233-0.14940.0157-0.11130.1116-0.03180.01630.24420.05840.325967.0589-71.7909-21.4635
16-0.0025-0.0066-0.02390.0064-0.0196-0.00080.05850.0094-0.03790.0226-0.0414-0.04990.068-0.10820.02420.0483-0.0998-0.0450.1912-0.0567-0.069765.8316-87.6037-29.229
170.00450.00290.00180.0111-0.00760.01040.0130.0189-0.10620.09740.00210.01910.04210.0875-0.03750.13920.0676-0.07680.3604-0.01330.222243.2923-87.272-25.0867
18-0.01060.0063-0.00980.0059-0.0013-0.01070.05980.1282-0.12070.09210.1243-0.1846-0.00340.1922-0.05340.0484-0.029-0.02210.2572-0.05440.205976.9157-82.3116-34.5282
190.03760.08840.01680.08890.06610.0133-0.05530.2512-0.0217-0.11310.0549-0.06790.04340.14440.01540.1666-0.049-0.0530.38270.00420.100775.2155-86.5276-41.6954
200.06510.02150.02960.00930.06840.0557-0.04810.3315-0.0544-0.04420.1698-0.0139-0.09110.1594-0.06050.3642-0.0978-0.02230.7460.04130.112272.7718-89.7944-58.357
210.1901-0.09920.06210.04260.0379-0.0089-0.01490.1233-0.14460.10010.11840.0212-0.10670.2331-0.03230.2235-0.0046-0.01350.8538-0.1120.018961.7865-106.8727-68.1924
220.06630.03230.00450.0657-0.014-0.01790.0784-0.1029-0.22420.05710.0493-0.13310.0763-0.02-0.03680.4277-0.0450.05320.7331-0.18530.178648.4234-107.6649-69.618
23-0.00520.01110.0192-0.0580.00310.07130.13120.00210.02230.0201-0.0956-0.01010.1256-0.09690.08030.30510.0197-0.0170.9612-0.2671-0.13841.8619-110.4952-72.7133
240.0472-0.00110.01050.00490.04130.06650.11080.03810.0187-0.0062-0.00540.0117-0.0265-0.07150.00090.4276-0.0155-0.28061.1868-0.21340.264625.7358-106.2048-67.3699
250.04210.0224-0.00130.0642-0.01070.06120.01170.124-0.0577-0.0751-0.0027-0.1596-0.01690.0809-0.00320.51790.0964-0.33880.7598-0.14250.541424.3947-81.212242.8573
260.90040.1449-0.66960.08230.05480.4569-0.3328-0.2445-0.01080.0941-0.12430.0282-0.1509-0.0305-0.05890.34770.0141-0.20790.4445-0.30880.370411.6369-83.167641.7825
270.11430.03160.07890.02230.1110.19390.044-0.04970.1578-0.0017-0.11810.1794-0.36520.19410.03440.288-0.0222-0.11460.2364-0.13220.39528.2773-82.896328.1685
280.0743-0.17410.1580.2422-0.03130.1743-0.042-0.10710.1215-0.02420.0719-0.0125-0.0533-0.012-0.0570.08340.0351-0.02910.1871-0.06920.345-1.1282-97.806513.8031
290.13560.00470.04630.01020.15210.10920.01190.04960.08620.04040.02970.0404-0.038-0.0648-0.03820.11420.02170.01360.1449-0.00540.3362-3.1955-119.62720.5046
300.1279-0.0842-0.06950.16450.09730.2247-0.0558-0.0087-0.15510.0444-0.06590.1927-0.0376-0.0120.10330.09890.0049-0.00320.13670.03310.305817.5852-136.27631.7365
310.0541-0.1790.03750.20670.20960.3810.0024-0.0913-0.02480.12410.1780.03460.14310.1645-0.01720.0580.07550.0130.19360.05680.237730.7909-142.229516.197
32-0.0156-0.01960.02680.0262-0.02520.02660.06610.11880.0134-0.0376-0.0245-0.1866-0.1152-0.0779-0.02310.0828-0.00550.05860.22280.01360.157929.7497-126.225823.8038
33-0.01710.0236-0.03580.0098-0.0079-0.0303-0.00590.002-0.0403-0.0087-0.13190.0078-0.2337-0.17210.03130.09360.0483-0.01310.5608-0.09490.43257.3518-126.567319.7191
340.07030.02590.0210.1586-0.0020.07750.0129-0.0523-0.0240.11910.1745-0.01860.12910.3311-0.05660.22930.1083-0.03340.1897-0.0570.167140.8328-131.511529.112
350.0218-0.13460.08680.24220.03590.12450.04840.1131-0.0614-0.03520.0389-0.233-0.09860.1565-0.00830.1040.077-0.05330.3602-0.02420.044439.1277-127.287436.2442
360.07970.0365-0.0523-0.0203-0.00910.13030.0558-0.0884-0.0010.16110.1585-0.16510.17140.1751-0.08710.33580.0615-0.06290.73110.08210.195236.72-124.04352.9186
370.35970.1464-0.02720.0469-0.01410.02770.0059-0.18420.21670.12040.00610.1040.0730.13060.02220.29610.05-0.05660.9192-0.10760.050125.6092-106.730762.8235
380.0330.00650.02430.0216-0.01840.01650.14830.0471-0.01210.04040.0641-0.00570.137-0.0951-0.03050.47820.1894-0.13330.8432-0.23140.158412.3823-106.137164.1913
390.10830.004-0.03530.10860.12720.097-0.1472-0.0119-0.0382-0.0475-0.04320.12110.0523-0.1668-0.11840.26210.07860.11940.9669-0.3284-0.25185.7673-103.299267.2551
400.055-0.0348-0.06860.0159-0.0657-0.03630.0989-0.02130.07170.0728-0.0959-0.03180.0010.00640.01080.34850.02220.06491.2759-0.05920.3554-10.1495-107.558862.0114
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain B and resid 1:39
2X-RAY DIFFRACTION2chain B and resid 40:290
3X-RAY DIFFRACTION3chain B and resid 330:365
4X-RAY DIFFRACTION4chain E and resid 1:39
5X-RAY DIFFRACTION5chain E and resid 40:290
6X-RAY DIFFRACTION6chain E and resid 330:365
7X-RAY DIFFRACTION7chain C
8X-RAY DIFFRACTION8chain F
9X-RAY DIFFRACTION9chain A and resid 1028:1055
10X-RAY DIFFRACTION10chain A and resid 969:1027
11X-RAY DIFFRACTION11chain A and resid 908:963
12X-RAY DIFFRACTION12chain A and resid 767:907
13X-RAY DIFFRACTION13chain A and resid 627:766
14X-RAY DIFFRACTION14chain A and resid 533:626
15X-RAY DIFFRACTION15chain A and resid 468:532
16X-RAY DIFFRACTION16chain A and resid 449:467
17X-RAY DIFFRACTION17chain A and resid 425:448
18X-RAY DIFFRACTION18chain A and resid 402:424
19X-RAY DIFFRACTION19chain A and resid 311:401
20X-RAY DIFFRACTION20chain A and resid 240:310
21X-RAY DIFFRACTION21chain A and resid 145:239
22X-RAY DIFFRACTION22chain A and resid 120:144
23X-RAY DIFFRACTION23chain A and resid 67:119
24X-RAY DIFFRACTION24chain A and resid 4:66
25X-RAY DIFFRACTION25chain D and resid 1028:1055
26X-RAY DIFFRACTION26chain D and resid 969:1027
27X-RAY DIFFRACTION27chain D and resid 908:963
28X-RAY DIFFRACTION28chain D and resid 767:907
29X-RAY DIFFRACTION29chain D and resid 627:766
30X-RAY DIFFRACTION30chain D and resid 533:626
31X-RAY DIFFRACTION31chain D and resid 468:532
32X-RAY DIFFRACTION32chain D and resid 449:467
33X-RAY DIFFRACTION33chain D and resid 425:448
34X-RAY DIFFRACTION34chain D and resid 402:424
35X-RAY DIFFRACTION35chain D and resid 311:401
36X-RAY DIFFRACTION36chain D and resid 240:310
37X-RAY DIFFRACTION37chain D and resid 145:239
38X-RAY DIFFRACTION38chain D and resid 120:144
39X-RAY DIFFRACTION39chain D and resid 67:119
40X-RAY DIFFRACTION40chain D and resid 4:66

+
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://pdbjlc1.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