[English] 日本語
Yorodumi
- PDB-5di9: Crystal Structure of hRio2 NES Reverse Mutant Peptide in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5di9
TitleCrystal Structure of hRio2 NES Reverse Mutant Peptide in complex with CRM1-Ran-RanBP1
Components
  • Engineered Nuclear Export Signal Peptide (hRio2 NES reverse mutant)
  • Exportin-1Karyopherin
  • GTP-binding nuclear protein Ran
  • Ran-specific GTPase-activating protein 1
KeywordsTRANSPORT PROTEIN / Peptides / HEAT repeat / Nuclear Export signal / Exportin-1 / Nuclear Transport
Function / homology
Function and homology information


MAPK6/MAPK4 signaling / RNA nuclear export complex / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / U4 snRNA binding ...MAPK6/MAPK4 signaling / RNA nuclear export complex / nuclear export signal receptor activity / pre-miRNA export from nucleus / snRNA import into nucleus / cellular response to mineralocorticoid stimulus / manchette / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / U4 snRNA binding / spindle pole body / RNA export from nucleus / protein localization to kinetochore / nuclear export / 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 / NLS-bearing protein import into nucleus / dynein intermediate chain binding / ribosomal subunit export from nucleus / spermatid development / mitotic sister chromatid segregation / ribosomal small subunit export from nucleus / ribosomal large subunit export from nucleus / U5 snRNA binding / sperm flagellum / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / nuclear pore / U1 snRNA binding / protein export from nucleus / centriole / viral process / GTPase activator activity / G protein activity / mitotic spindle organization / male germ cell nucleus / hippocampus development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Transcriptional regulation by small RNAs / G1/S transition of mitotic cell cycle / kinetochore / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / mitotic cell cycle / nuclear envelope / positive regulation of protein binding / midbody / ubiquitin-dependent protein catabolic process / actin cytoskeleton organization / cadherin binding / protein heterodimerization activity / cell division / protein domain specific binding / GTPase activity / chromatin binding / chromatin / GTP binding / nucleolus / perinuclear region of cytoplasm / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Ran-specific GTPase-activating protein 1, Ran-binding domain / 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 ...Ran-specific GTPase-activating protein 1, Ran-binding domain / 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 / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 / Small GTP-binding protein domain / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Exportin-1 / Ran-specific GTPase-activating protein 1 / GTP-binding nuclear protein Ran
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsFung, H.Y. / Chook, Y.M.
Funding support Hong Kong, United States, 6items
OrganizationGrant numberCountry
Croucher FoundationStudent Scholarship Hong Kong
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069909 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP120352 United States
University of Texas SouthwesternEndowed Scholars Program United States
Welch FoundationI-1532 United States
Leukemia & Lymphoma SocietyScholar Award United States
CitationJournal: Elife / Year: 2015
Title: Structural determinants of nuclear export signal orientation in binding to exportin CRM1.
Authors: Fung, H.Y. / Fu, S.C. / Brautigam, C.A. / Chook, Y.M.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTP-binding nuclear protein Ran
B: Ran-specific GTPase-activating protein 1
C: Exportin-1
D: Engineered Nuclear Export Signal Peptide (hRio2 NES reverse mutant)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,19712
Polymers163,1824
Non-polymers1,0168
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12010 Å2
ΔGint-111 kcal/mol
Surface area57770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.692, 106.692, 304.497
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein GTP-binding nuclear protein Ran / Androgen receptor-associated protein 24 / GTPase Ran / Ras-like protein TC4 / Ras-related nuclear protein


Mass: 26758.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAN, ARA24, OK/SW-cl.81 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL219(DE3) / References: UniProt: P62826
#2: Protein Ran-specific GTPase-activating protein 1 / Chromosome stability protein 20 / Perinuclear array-localized protein / Ran-binding protein 1 / RANBP1


Mass: 16521.867 Da / Num. of mol.: 1 / Fragment: RanDB1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: YRB1, CST20, HTN1, SFO1, YDR002W, YD8119.08 / Plasmid: pGex4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41920
#3: Protein Exportin-1 / Karyopherin / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 117458.781 Da / Num. of mol.: 1
Mutation: V441D,D536G,T539C,V540E,K541Q,Y1022C, delta 377-413
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CRM1, KAP124, XPO1, YGR218W, G8514 / Plasmid: pGex4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30822

-
Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide Engineered Nuclear Export Signal Peptide (hRio2 NES reverse mutant)


Mass: 2442.496 Da / Num. of mol.: 1 / Fragment: Nuclear Export Signal
Source method: isolated from a genetically manipulated source
Details: Engineered mutant sequence of CPEPB4 NES / Source: (gene. exp.) Homo sapiens (human) / Gene: CPEB4 / Plasmid: pMal / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

-
Non-polymers , 6 types, 366 molecules

#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.66 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 17% PEG3350, 100mM Bis-Tris pH6.4, 200mM NH4NO3, 10mM Spermine HCl

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2015
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 127043 / % possible obs: 98 % / Redundancy: 7 % / Biso Wilson estimate: 28.49 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Χ2: 0.899 / Net I/av σ(I): 22.5 / Net I/σ(I): 8.3 / Num. measured all: 557247
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.28-2.3270.97139740.7760.3860.92199.2
2.32-2.366.90.82739590.80.330.91499.10.892
2.36-2.4170.71839480.8550.2850.92199.20.774
2.41-2.4670.63539270.8890.2520.909990.685
2.46-2.5170.5439770.9120.2140.892990.582
2.51-2.5770.45139650.9380.1780.89698.90.486
2.57-2.6370.38339670.9510.1520.89198.80.413
2.63-2.770.33239760.9610.1310.89798.80.358
2.7-2.7870.26839850.9680.1060.86798.70.289
2.78-2.8770.21439590.9810.0840.85798.60.231
2.87-2.9870.17639780.9860.0690.85498.50.19
2.98-3.0970.1439760.990.0550.8698.30.15
3.09-3.247.10.10739790.9930.0420.86398.10.115
3.24-3.4170.08739660.9940.0340.9297.90.094
3.41-3.6270.07339820.9940.0291.05897.60.079
3.62-3.970.06639740.9950.0261.24797.40.071
3.9-4.2970.05239980.9970.021.12996.90.056
4.29-4.916.80.03940060.9980.0150.93696.60.042
4.91-6.1970.03240470.9990.0130.62196.20.035
6.19-506.70.02541840.9990.010.52493.40.027

-
Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HB2
Resolution: 2.28→37.721 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 3179 2.5 %Random selection
Rwork0.1683 123864 --
obs0.1694 127043 82.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.93 Å2 / Biso mean: 43.9482 Å2 / Biso min: 14.35 Å2
Refinement stepCycle: final / Resolution: 2.28→37.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10876 0 59 358 11293
Biso mean--46.41 35.44 -
Num. residues----1347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611243
X-RAY DIFFRACTIONf_angle_d0.83515214
X-RAY DIFFRACTIONf_chiral_restr0.0321730
X-RAY DIFFRACTIONf_plane_restr0.0031934
X-RAY DIFFRACTIONf_dihedral_angle_d13.2494202
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2786-2.31260.2764860.24743267335350
2.3126-2.34870.2935860.23293340342652
2.3487-2.38720.2811890.23493481357053
2.3872-2.42840.2303920.22793607369955
2.4284-2.47250.2531960.223709380557
2.4725-2.52010.26111000.2114011411162
2.5201-2.57150.27011130.20464301441466
2.5715-2.62740.24971290.20514671480072
2.6274-2.68850.22181280.20845289541781
2.6885-2.75570.27641580.20495932609091
2.7557-2.83020.2441490.21136273642296
2.8302-2.91350.23891660.20236381654798
2.9135-3.00750.27141620.19326405656799
3.0075-3.11490.20861640.19436371653598
3.1149-3.23960.27741680.18866399656798
3.2396-3.38690.2051630.18146360652398
3.3869-3.56540.211650.17166411657698
3.5654-3.78860.18681660.15236309647597
3.7886-4.08080.17031590.14336305646497
4.0808-4.49080.17421560.12366278643497
4.4908-5.13930.16011660.11796288645497
5.1393-6.46960.21781570.15136295645297
6.4696-37.72650.18121610.13956181634295
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)
12.1792-0.84440.80722.14581.5235.7302-0.25950.23970.0524-0.28290.2785-0.5268-0.41520.4633-0.04740.1736-0.02410.00680.2771-0.07440.36267.960844.497437.9198
22.0016-1.927-0.15182.60221.1921.48660.01950.5517-0.1773-0.69180.0408-0.3757-0.26360.4027-0.08830.2745-0.08110.13610.4452-0.14340.39337.24846.49925.2007
31.2671-0.8157-0.05844.61680.70842.47010.1290.12940.0576-0.09850.2134-0.8685-0.54350.6305-0.34430.2326-0.10870.06820.367-0.12640.514311.771953.095538.1109
42.0295-1.0146-0.36731.0669-0.38130.63390.05090.3052-0.3680.00150.0267-0.53250.08220.3252-0.08340.14310.0268-0.03170.2959-0.11660.54518.118737.280437.2095
51.0173-0.3544-0.23922.7464-1.08093.770.02450.126-0.4033-0.18990.0418-0.20280.34320.068-0.04510.13480.0375-0.00420.2134-0.07330.3393-1.558434.165538.7031
61.08080.0273-1.46863.223-0.81153.79170.00130.1038-0.0288-0.10610.0460.0528-0.0256-0.4455-0.03510.15880.0211-0.0140.2492-0.06630.257-6.935542.979338.418
72.18810.24520.88413.18910.61574.150.02340.02180.2891-0.2332-0.0142-0.0605-0.89060.0278-0.00320.34410.00050.02540.2516-0.03620.31580.599556.658638.9399
84.61190.6502-0.264.08380.20753.3048-0.19250.6476-0.2114-0.76970.5101-0.89540.27020.0138-0.24350.8215-0.60520.19181.191-0.31080.638220.03373.817320.4525
95.09311.3112-0.85911.7514-1.26171.91940.5156-0.01410.3294-0.620.2853-1.0466-0.16580.7118-0.70230.7424-0.16540.20921.1263-0.31090.743818.772862.71244.5044
104.1604-0.72180.69195.30170.29973.0298-0.1641-0.12610.09020.07290.31180.30080.1551-0.2846-0.12570.3838-0.13530.1140.4362-0.09840.5148-1.501656.414212.0608
110.96550.52490.10830.8028-0.50620.6216-0.10080.04320.06870.11680.0102-0.3045-0.26580.30420.07750.9675-0.2504-0.03050.5864-0.05290.70043.44680.75946.6365
123.3643-0.18450.43825.03410.34412.67880.03650.0261-0.15840.28270.07710.0775-0.28570.6512-0.07740.4299-0.16090.13950.4647-0.01050.35666.945863.246517.37
130.59450.47140.12971.1730.05380.0418-0.1070.05650.1171-0.0232-0.00170.2281-1.01530.77210.10.7646-0.34140.18070.4779-0.0230.43877.476471.381319.573
142.76572.14470.12053.0881.38861.1917-0.16570.05820.2291-0.4130.17210.1041-1.01390.71150.04350.656-0.27870.11760.5495-0.04020.45117.864371.415913.8068
151.518-0.1122-0.06881.76850.42990.994-0.1242-0.13060.01060.55710.2434-0.76260.34790.3687-0.02630.25160.1315-0.24950.3438-0.07170.60359.994324.882253.1037
162.0351-0.82510.62582.2542-0.48253.0385-0.00610.0055-0.07990.08090.05840.0394-0.0008-0.2417-0.05380.1717-0.0008-0.00360.2261-0.06290.1301-22.843747.136754.8582
171.2152-0.42180.2341.7124-0.00493.37140.23140.05510.229-0.21-0.0489-0.0924-0.7695-0.3868-0.14150.49440.17690.06420.37490.01880.2449-34.10466.753426.1686
182.8382-1.3174-0.55511.84850.44231.83760.03470.21530.1282-0.25890.0991-0.0232-0.3579-0.1605-0.14250.30360.04320.03990.30760.02180.1533-22.35651.2526-1.1383
190.8541-0.82170.98331.4739-1.76712.72080.14840.0797-0.3198-0.1390.0970.28110.18440.0082-0.21390.19110.01410.02320.2501-0.09190.3284-8.825117.542614.5434
204.21862.0506-1.27365.5361-1.57124.69040.0556-0.07490.6318-0.48180.18050.5672-0.7589-0.2746-0.25490.95490.35360.05170.57280.06930.4429-38.971475.974728.4107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 22 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 44 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 66 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 91 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 92 through 111 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 148 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 149 through 179 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 190 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 191 through 206 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 207 through 216 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 65 through 82 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 83 through 106 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 107 through 154 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 155 through 200 )B0
15X-RAY DIFFRACTION15chain 'C' and (resid 0 through 245 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 246 through 495 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 496 through 637 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 638 through 808 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 809 through 1052 )C0
20X-RAY DIFFRACTION20chain 'D' and (resid 5 through 20 )D0

+
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