[English] 日本語
Yorodumi
- PDB-5dlq: Crystal structure of RanGTP-Exportin 4-eIF5A complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dlq
TitleCrystal structure of RanGTP-Exportin 4-eIF5A complex
Components
  • Eukaryotic translation initiation factor 5A-1
  • Exportin-4
  • GTP-binding nuclear protein Ran
KeywordsPROTEIN TRANSPORT / Active transport / Nuclear transport / Nuclear export Importin-Beta family / Exportin / HEAT repeat / GTPase / Nucleotide binding / eIF5A / Translation factor / Hypusine / Unusual amino acid
Function / homology
Function and homology information


Hypusine synthesis from eIF5A-lysine / positive regulation of translational termination / annulate lamellae / positive regulation of translational elongation / RNA nuclear export complex / pre-miRNA export from nucleus / nuclear export signal receptor activity / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette ...Hypusine synthesis from eIF5A-lysine / positive regulation of translational termination / annulate lamellae / positive regulation of translational elongation / RNA nuclear export complex / 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 / 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 / translational elongation / DNA metabolic process / dynein intermediate chain binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / ribosomal small subunit export from nucleus / translation elongation factor activity / U6 snRNA binding / ribosomal subunit export from nucleus / nuclear pore / tumor necrosis factor-mediated signaling pathway / centriole / protein export from nucleus / viral process / positive regulation of 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 / cellular response to virus / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / ribosome binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / chromatin / endoplasmic reticulum membrane / nucleolus / GTP binding / magnesium ion binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Exportin 4/7-like / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / small GTPase Ran family profile. ...Exportin 4/7-like / : / Translation initiation factor 5A-like, N-terminal / Translation elongation factor, IF5A, hypusine site / Eukaryotic initiation factor 5A hypusine signature. / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / Translation elongation factor IF5A-like / Translation elongation factor, IF5A C-terminal / Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold / small GTPase Ran family profile. / Ran GTPase / SH3 type barrels. - #30 / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Nucleic acid-binding proteins / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / SH3 type barrels. / Armadillo-like helical / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Small GTP-binding protein domain / Translation protein SH3-like domain superfamily / Armadillo-type fold / Ribosomal protein L2, domain 2 / P-loop containing nucleotide triphosphate hydrolases / Roll / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTP-binding nuclear protein Ran / Eukaryotic translation initiation factor 5A-1 / Exportin-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsAksu, M. / Trakhanov, S. / Gorlich, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: Nat Commun / Year: 2016
Title: Structure of the exportin Xpo4 in complex with RanGTP and the hypusine-containing translation factor eIF5A.
Authors: Aksu, M. / Trakhanov, S. / Gorlich, D.
History
DepositionSep 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Exportin-4
C: GTP-binding nuclear protein Ran
F: Eukaryotic translation initiation factor 5A-1
A: Exportin-4
D: GTP-binding nuclear protein Ran
E: Eukaryotic translation initiation factor 5A-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,44410
Polymers323,3496
Non-polymers1,0954
Water00
1
B: Exportin-4
C: GTP-binding nuclear protein Ran
F: Eukaryotic translation initiation factor 5A-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,2225
Polymers161,6743
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7930 Å2
ΔGint-29 kcal/mol
Surface area58630 Å2
MethodPISA
2
A: Exportin-4
D: GTP-binding nuclear protein Ran
E: Eukaryotic translation initiation factor 5A-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,2225
Polymers161,6743
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-28 kcal/mol
Surface area57920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.616, 98.616, 726.864
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
11(chain C and (resseq 7:75 or (resid 76 and (name...
21(chain D and (resseq 7:33 or (resid 34 and (name...
12(chain A and (resseq 9 or (resid 10 and (name...
22(chain B and (resseq 9 or (resid 10 and (name...
13(chain E and (resseq 16:67 or (resid 68 and (name...
23(chain F and (resseq 16:17 or (resid 18 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain C and (resseq 7:75 or (resid 76 and (name...C7 - 75
121(chain C and (resseq 7:75 or (resid 76 and (name...C76
131(chain C and (resseq 7:75 or (resid 76 and (name...C7 - 179
141(chain C and (resseq 7:75 or (resid 76 and (name...C7 - 179
151(chain C and (resseq 7:75 or (resid 76 and (name...C7 - 179
161(chain C and (resseq 7:75 or (resid 76 and (name...C7 - 179
211(chain D and (resseq 7:33 or (resid 34 and (name...D7 - 33
221(chain D and (resseq 7:33 or (resid 34 and (name...D34
231(chain D and (resseq 7:33 or (resid 34 and (name...D7 - 178
241(chain D and (resseq 7:33 or (resid 34 and (name...D7 - 178
251(chain D and (resseq 7:33 or (resid 34 and (name...D7 - 178
261(chain D and (resseq 7:33 or (resid 34 and (name...D7 - 178
112(chain A and (resseq 9 or (resid 10 and (name...A9
122(chain A and (resseq 9 or (resid 10 and (name...A10
132(chain A and (resseq 9 or (resid 10 and (name...A9 - 1145
142(chain A and (resseq 9 or (resid 10 and (name...A9 - 1145
152(chain A and (resseq 9 or (resid 10 and (name...A9 - 1145
212(chain B and (resseq 9 or (resid 10 and (name...B9
222(chain B and (resseq 9 or (resid 10 and (name...B10
232(chain B and (resseq 9 or (resid 10 and (name...B4 - 1148
242(chain B and (resseq 9 or (resid 10 and (name...B4 - 1148
252(chain B and (resseq 9 or (resid 10 and (name...B4 - 1148
113(chain E and (resseq 16:67 or (resid 68 and (name...E16 - 67
123(chain E and (resseq 16:67 or (resid 68 and (name...E68
133(chain E and (resseq 16:67 or (resid 68 and (name...E16 - 152
143(chain E and (resseq 16:67 or (resid 68 and (name...E16 - 152
153(chain E and (resseq 16:67 or (resid 68 and (name...E16 - 152
163(chain E and (resseq 16:67 or (resid 68 and (name...E16 - 152
173(chain E and (resseq 16:67 or (resid 68 and (name...E16 - 152
213(chain F and (resseq 16:17 or (resid 18 and (name...F16 - 17
223(chain F and (resseq 16:17 or (resid 18 and (name...F18
233(chain F and (resseq 16:17 or (resid 18 and (name...F15 - 152
243(chain F and (resseq 16:17 or (resid 18 and (name...F15 - 152
253(chain F and (resseq 16:17 or (resid 18 and (name...F15 - 152
263(chain F and (resseq 16:17 or (resid 18 and (name...F15 - 152

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Exportin-4 / Exp4


Mass: 125894.023 Da / Num. of mol.: 2 / Mutation: H1085Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Xpo4, Kiaa1721 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): Top10 F' / References: UniProt: Q9ESJ0
#2: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 20192.484 Da / Num. of mol.: 2 / Mutation: Q69L
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 K-12 (bacteria) / Variant (production host): Top10 F' / References: UniProt: P62826
#3: Protein Eukaryotic translation initiation factor 5A-1 / eIF-5A1 / Eukaryotic initiation factor 5A isoform 1 / eIF-5A / Rev-binding factor / eIF-4D


Mass: 15587.991 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF5A / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): NEB express / References: UniProt: P63241
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.1661.08
23.1661.1
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop6.26Peg 400, MES
2932vapor diffusion, hanging drop6.26Peg 400, MES, DTT

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA11
SYNCHROTRONSLS X10SA20.9786
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M-F1PIXELJun 13, 2014
DECTRIS PILATUS 6M-F2PIXELJul 10, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.987641
211
30.97861
ReflectionResolution: 3→49.407 Å / Num. obs: 157964 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 106.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.097 / Χ2: 1.008 / Net I/σ(I): 14.55 / Num. measured all: 828210
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3-3.0810.21.6120.995847411673115580.4551.899
3.08-3.161.1291.476189211428114260.6591.251100
3.16-3.250.8671.895916311019110180.7730.962100
3.25-3.350.6162.625696210795107940.8340.685100
3.35-3.460.4473.555276110386103770.9020.49999.9
3.46-3.590.3414.735264610113101120.940.379100
3.59-3.720.266.2252827977197710.9650.288100
3.72-3.870.1818.6750739939993990.9830.2100
3.87-4.050.1410.9847266897489740.9880.155100
4.05-4.240.10613.7442961860786000.9920.11999.9
4.24-4.470.08317.2841815824882440.9950.092100
4.47-4.740.06721.3241014773477330.9970.075100
4.74-5.070.0623.738047717871750.9970.067100
5.07-5.480.06223.0235508687868760.9970.069100
5.48-60.05824.9131723612561250.9970.064100
6-6.710.0529.131212566456640.9980.056100
6.71-7.750.03439.9526220493849340.9990.03899.9
7.75-9.490.02157.39209114188418510.02499.9
9.49-13.420.01676.6172853240324010.018100
13.420.01479.0387841790175910.01598.3

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→49.407 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 3494 5 %
Rwork0.2211 66335 -
obs0.2235 69829 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.92 Å2 / Biso mean: 118.5607 Å2 / Biso min: 55 Å2
Refinement stepCycle: final / Resolution: 3.2→49.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20622 0 66 0 20688
Biso mean--76.87 --
Num. residues----2655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221055
X-RAY DIFFRACTIONf_angle_d0.50428592
X-RAY DIFFRACTIONf_chiral_restr0.0373383
X-RAY DIFFRACTIONf_plane_restr0.0033624
X-RAY DIFFRACTIONf_dihedral_angle_d9.54112654
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C1575X-RAY DIFFRACTION9.818TORSIONAL
12D1575X-RAY DIFFRACTION9.818TORSIONAL
21A8595X-RAY DIFFRACTION9.818TORSIONAL
22B8595X-RAY DIFFRACTION9.818TORSIONAL
31E1217X-RAY DIFFRACTION9.818TORSIONAL
32F1217X-RAY DIFFRACTION9.818TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2001-3.2440.33191360.30625742710100
3.244-3.29030.41681420.294826882830100
3.2903-3.33940.3371330.276525182651100
3.3394-3.39160.28581390.264826422781100
3.3916-3.44720.33571350.266425622697100
3.4472-3.50660.33531380.268726322770100
3.5066-3.57030.28511370.266426012738100
3.5703-3.6390.33091390.266426362775100
3.639-3.71320.32991360.256925872723100
3.7132-3.7940.33241400.237326632803100
3.794-3.88220.25641350.232125592694100
3.8822-3.97920.27111380.216326372775100
3.9792-4.08680.2611400.222226462786100
4.0868-4.2070.30961350.223125782713100
4.207-4.34270.2581410.218226782819100
4.3427-4.49780.26171420.193726892831100
4.4978-4.67770.23271360.188125952731100
4.6777-4.89040.25831410.19226652806100
4.8904-5.1480.26421390.20226552794100
5.148-5.47020.26381420.217226882830100
5.4702-5.89190.28271400.239326662806100
5.8919-6.48370.29351430.24827072850100
6.4837-7.41910.26721440.239427502894100
7.4191-9.3370.19671460.178327642910100
9.337-49.41290.25381570.21022955311299
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)
13.06021.0165-0.37791.632-0.5622.9374-0.10430.9269-0.1777-0.3683-0.03090.03550.0969-0.32820.00220.44660.067-0.06510.998-0.08720.653414.086750.4646797.5276
23.7031-0.67360.07162.0930.43350.22360.020.65260.78370.403-0.0219-0.1416-0.90140.0667-0.02250.9354-0.24580.03511.16270.36470.887247.520967.5291796.4257
33.2034-0.5377-0.12481.7268-0.64321.73210.11170.53240.292-0.1847-0.1552-0.0493-0.57860.5559-0.2460.6628-0.35450.02931.10920.21670.761466.283462.3473805.5216
43.4025-1.0049-0.49142.6387-1.72431.551-0.18210.3198-0.00610.1265-0.2254-0.44360.22920.4854-0.00750.5052-0.21430.03361.1640.00670.889573.064447.7387813.0182
54.70271.4444-0.74722.9514-0.54583.25080.103-0.2872-0.30090.4771-0.138-0.36890.15820.2659-0.00150.5319-0.0532-0.10680.77660.04210.767361.399729.7011830.9725
62.49581.97632.1471.53041.67731.83630.5197-0.4349-0.23820.6357-0.4569-0.46790.3967-0.46950.00010.6978-0.2082-0.09520.64740.17870.885637.878419.3439826.7505
71.89570.03650.5341.27390.97182.6333-0.20781.0786-0.1689-0.82570.06670.9796-0.1830.0783-0.56611.0263-0.2964-0.1750.9998-0.13981.390717.495216.0198813.3165
83.98870.34760.40573.0755-0.20892.57370.20130.1316-0.2012-0.0028-0.1452-0.1642-0.1420.171300.4932-0.16550.02780.7414-0.01320.790327.588153.8965819.2743
94.33650.6473-0.85153.09540.17913.71820.0732-0.46880.29680.0016-0.3738-0.05510.1576-0.136400.99220.1364-0.03421.0637-0.02850.850547.385613.0992754.845
101.98180.5006-1.27551.9356-0.28440.7838-0.5122-0.1859-0.6283-0.6609-0.03760.09351.09691.26620.00011.56690.22430.10981.58130.16331.146977.681811.1712752.4902
111.3650.7646-0.59982.04370.38561.89580.02630.12120.1485-0.70180.01950.26960.1252-0.182-0.00011.61470.04140.22011.70560.14091.376183.526926.8083727.4372
121.48-1.74780.50292.3934-0.64592.77010.3525-0.40750.07640.2981-0.31550.6024-0.02720.25560.00011.1554-0.2455-0.04341.0630.08121.054445.194432.0034858.21
131.04870.2612-0.30961.7746-1.02982.3283-0.0341-0.06270.33420.1517-0.1173-0.3496-0.83140.54130.00020.8536-0.16340.01030.91620.0560.948351.471853.4246837.4572
141.4074-0.66630.82241.5094-0.4264.42590.0684-0.2724-0.0289-0.0131-0.29790.4249-0.0686-1.0815-0.00460.6176-0.0640.04671.4607-0.32520.897624.911718.9392766.5987
152.25021.3587-0.03660.95680.14390.1678-0.1546-0.4999-0.4177-0.171-0.17210.27850.57410.0958-0.00041.64270.2670.18711.5750.25741.032452.19466.1904788.4944
162.83930.2451-1.05970.84890.66492.8651-0.1214-1.211-0.33090.1229-0.08150.01850.55541.175-0.09021.23480.28740.08122.09040.36131.040972.813511.1771788.9303
170.63070.9039-0.08691.2636-0.28690.6963-0.0174-0.3110.40150.0212-0.0801-0.3821-0.70332.05-0.00031.23990.0503-0.12322.3633-0.05350.993383.508823.8152783.1382
182.20311.27960.82252.3795-1.15041.96980.31140.04890.3212-0.1852-0.2747-0.0589-0.25470.7648-00.8788-0.17350.13991.7196-0.12520.999182.568836.4163756.6644
191.1279-0.6676-0.41380.8289-0.40531.09440.21760.45010.1612-0.1173-0.5997-0.38960.2405-0.56620.00021.23710.19720.07710.9463-0.0191.201661.300144.9222747.9846
202.12170.96120.92151.34660.19230.4326-0.1257-0.952-0.0929-0.1641-0.00720.5076-0.7876-0.82720.00171.35390.6131-0.07591.736-0.12351.222936.308749.2687749.4132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 4 through 364 )B4 - 364
2X-RAY DIFFRACTION2chain 'B' and (resid 365 through 460 )B365 - 460
3X-RAY DIFFRACTION3chain 'B' and (resid 461 through 646 )B461 - 646
4X-RAY DIFFRACTION4chain 'B' and (resid 647 through 744 )B647 - 744
5X-RAY DIFFRACTION5chain 'B' and (resid 745 through 924 )B745 - 924
6X-RAY DIFFRACTION6chain 'B' and (resid 949 through 1015 )B949 - 1015
7X-RAY DIFFRACTION7chain 'B' and (resid 1016 through 1148 )B0
8X-RAY DIFFRACTION8chain 'C'C7 - 179
9X-RAY DIFFRACTION9chain 'D'D7 - 178
10X-RAY DIFFRACTION10chain 'E' and (resid 16 through 83 )E16 - 83
11X-RAY DIFFRACTION11chain 'E' and (resid 84 through 152 )E84 - 152
12X-RAY DIFFRACTION12chain 'F' and (resid 84 through 152 )F84 - 152
13X-RAY DIFFRACTION13chain 'F' and (resid 15 through 83 )F15 - 83
14X-RAY DIFFRACTION14chain 'A' and (resid 9 through 364 )A9 - 364
15X-RAY DIFFRACTION15chain 'A' and (resid 365 through 451 )A365 - 451
16X-RAY DIFFRACTION16chain 'A' and (resid 460 through 646 )A460 - 646
17X-RAY DIFFRACTION17chain 'A' and (resid 647 through 744 )A647 - 744
18X-RAY DIFFRACTION18chain 'A' and (resid 745 through 922 )A745 - 922
19X-RAY DIFFRACTION19chain 'A' and (resid 952 through 1015 )A952 - 1015
20X-RAY DIFFRACTION20chain 'A' and (resid 1016 through 1145 )A0

+
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://pdbjlvh1.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