[English] 日本語
Yorodumi
- PDB-4x4p: Crystal structure of the A.fulgidus CCA-adding enzyme in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x4p
TitleCrystal structure of the A.fulgidus CCA-adding enzyme in complex with a G70A arginyl-tRNA minihelix ending in CCAC
Components
  • CCA-adding enzyme
  • G70A tRNA minihelix ending in CCAC
KeywordsRNA BINDING PROTEIN / protein-RNA complex / tRNA / non-coding RNA / CCA-adding enzyme / nucleotidyltransferase / ncRNA
Function / homology
Function and homology information


tRNA surveillance / CCACCA tRNA nucleotidyltransferase activity / CCA tRNA nucleotidyltransferase / tRNA 3'-terminal CCA addition / RNA repair / tRNA binding / magnesium ion binding / ATP binding
Similarity search - Function
CCA tRNA nucleotidyltransferase, domain 2 / Archaeal tRNA CCA-adding enzyme catalytic domain / tRNA nucleotidyltransferase, archaea / tRNA nucleotidyltransferase, substrate binding / tRNA nucleotidyltransferase, domain 2 / : / tRNA nucleotidyltransferase, second domain / CCA-adding enzyme, C-terminal domain / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal ...CCA tRNA nucleotidyltransferase, domain 2 / Archaeal tRNA CCA-adding enzyme catalytic domain / tRNA nucleotidyltransferase, archaea / tRNA nucleotidyltransferase, substrate binding / tRNA nucleotidyltransferase, domain 2 / : / tRNA nucleotidyltransferase, second domain / CCA-adding enzyme, C-terminal domain / Poly(A) polymerase predicted RNA binding domain / Nucleotidyltransferase, class I-like, C-terminal / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Poly(a)-polymerase, middle domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / CCA-adding enzyme
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 3 Å
AuthorsKuhn, C.-D. / Joshua-Tor, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2015
Title: On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme.
Authors: Kuhn, C.D. / Wilusz, J.E. / Zheng, Y. / Beal, P.A. / Joshua-Tor, L.
History
DepositionDec 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_entity_src_syn ...entity_src_gen / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CCA-adding enzyme
B: G70A tRNA minihelix ending in CCAC
C: CCA-adding enzyme
D: G70A tRNA minihelix ending in CCAC
E: CCA-adding enzyme
F: G70A tRNA minihelix ending in CCAC
G: CCA-adding enzyme
H: G70A tRNA minihelix ending in CCAC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,90218
Polymers260,9428
Non-polymers96110
Water00
1
A: CCA-adding enzyme
B: G70A tRNA minihelix ending in CCAC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7167
Polymers65,2352
Non-polymers4805
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-93 kcal/mol
Surface area28070 Å2
MethodPISA
2
C: CCA-adding enzyme
D: G70A tRNA minihelix ending in CCAC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3313
Polymers65,2352
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-36 kcal/mol
Surface area27440 Å2
MethodPISA
3
E: CCA-adding enzyme
F: G70A tRNA minihelix ending in CCAC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4284
Polymers65,2352
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-47 kcal/mol
Surface area26970 Å2
MethodPISA
4
G: CCA-adding enzyme
H: G70A tRNA minihelix ending in CCAC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4284
Polymers65,2352
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-42 kcal/mol
Surface area27120 Å2
MethodPISA
5
A: CCA-adding enzyme
B: G70A tRNA minihelix ending in CCAC
C: CCA-adding enzyme
D: G70A tRNA minihelix ending in CCAC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,04710
Polymers130,4714
Non-polymers5766
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint-142 kcal/mol
Surface area50670 Å2
MethodPISA
6
E: CCA-adding enzyme
F: G70A tRNA minihelix ending in CCAC
G: CCA-adding enzyme
H: G70A tRNA minihelix ending in CCAC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8558
Polymers130,4714
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-103 kcal/mol
Surface area49280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.108, 58.112, 217.806
Angle α, β, γ (deg.)85.200, 87.980, 89.810
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 3:89 or resseq 97:121 or resseq 123:437 )
21chain C and (resseq 3:89 or resseq 97:121 or resseq 123:437 )
31chain E and (resseq 3:89 or resseq 97:121 or resseq 123:437 )
41chain G and (resseq 3:89 or resseq 97:121 or resseq 123:437 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 3:89 or resseq 97:121 or resseq 123:437 )A3 - 89
121chain A and (resseq 3:89 or resseq 97:121 or resseq 123:437 )A97 - 121
131chain A and (resseq 3:89 or resseq 97:121 or resseq 123:437 )A123 - 437
211chain C and (resseq 3:89 or resseq 97:121 or resseq 123:437 )C3 - 89
221chain C and (resseq 3:89 or resseq 97:121 or resseq 123:437 )C97 - 121
231chain C and (resseq 3:89 or resseq 97:121 or resseq 123:437 )C123 - 437
311chain E and (resseq 3:89 or resseq 97:121 or resseq 123:437 )E3 - 89
321chain E and (resseq 3:89 or resseq 97:121 or resseq 123:437 )E97 - 121
331chain E and (resseq 3:89 or resseq 97:121 or resseq 123:437 )E123 - 437
411chain G and (resseq 3:89 or resseq 97:121 or resseq 123:437 )G3 - 89
421chain G and (resseq 3:89 or resseq 97:121 or resseq 123:437 )G97 - 121
431chain G and (resseq 3:89 or resseq 97:121 or resseq 123:437 )G123 - 437

-
Components

#1: Protein
CCA-adding enzyme / CCA tRNA nucleotidyltransferase / tRNA CCA-pyrophosphorylase / tRNA adenylyl-/cytidylyl- ...CCA tRNA nucleotidyltransferase / tRNA CCA-pyrophosphorylase / tRNA adenylyl-/cytidylyl- transferase / tRNA nucleotidyltransferase / tRNA-NT


Mass: 53672.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: cca, AF_2156 / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL
References: UniProt: O28126, CCA tRNA nucleotidyltransferase
#2: RNA chain
G70A tRNA minihelix ending in CCAC


Mass: 11562.915 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 30% 2-Propanol, 0.1M Sodium Acetate pH 5.3, 0.2M Lithium Sulfate, 4.8% PEG 1.5K
PH range: 5.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.13
ReflectionResolution: 3→29.576 Å / Num. obs: 53506 / % possible obs: 94.1 % / Redundancy: 2 % / Rpim(I) all: 0.073 / Rrim(I) all: 0.109 / Rsym value: 0.081 / Net I/av σ(I): 8.767 / Net I/σ(I): 9.1 / Num. measured all: 107845
Reflection shell

Diffraction-ID: 1 / Redundancy: 2 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3-3.160.3482.21646280900.3170.3482.596.4
3.16-3.350.2263.31504674520.2070.2263.996
3.35-3.590.1534.91434370190.1380.1535.994.3
3.59-3.870.1047.11297464530.0950.1048.393.6
3.87-4.240.0789.51151057490.0710.07810.492.3
4.24-4.740.05712.91050052320.0510.05713.691.3
4.74-5.480.05313.5946147270.0480.0531493.2
5.48-6.710.05613.2814140010.050.05612.894.6
6.71-9.490.03618.2615331370.0330.03617.494.6
9.49-29.5760.02622.9325516460.0230.0262391.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
XDSdata reduction
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementResolution: 3→29.576 Å / Cross valid method: FREE R-VALUE / σ(F): 0.96 / Phase error: 33.84 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2738 4210 4.33 %
Rwork0.2235 93504 -
obs0.2257 -85.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 252.67 Å2 / Biso mean: 69.3324 Å2 / Biso min: 22.02 Å2
Refinement stepCycle: final / Resolution: 3→29.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14332 2609 50 0 16991
Biso mean--62.05 --
Num. residues----1849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717601
X-RAY DIFFRACTIONf_angle_d1.09324273
X-RAY DIFFRACTIONf_chiral_restr0.0442658
X-RAY DIFFRACTIONf_plane_restr0.0062681
X-RAY DIFFRACTIONf_dihedral_angle_d13.5487085
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8601X-RAY DIFFRACTION7.68TORSIONAL
12C8601X-RAY DIFFRACTION7.68TORSIONAL
13E8601X-RAY DIFFRACTION7.68TORSIONAL
14G8601X-RAY DIFFRACTION7.68TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.05170.36532000.30364741494181
3.0517-3.10710.41540.29894803495787
3.1071-3.16680.35852060.29384811501784
3.1668-3.23130.31461900.27834903509385
3.2313-3.30140.31861740.27494371454580
3.3014-3.37810.32611890.26164942513186
3.3781-3.46240.29091770.25424726490383
3.4624-3.55580.27561980.23834603480182
3.5558-3.66010.28091880.23744581476980
3.6601-3.7780.23921840.22654561474581
3.778-3.91260.2851730.22234855502883
3.9126-4.06870.25021760.22434436461280
4.0687-4.25320.30891650.21184538470381
4.2532-4.47640.28651930.20954732492581
4.4764-4.75530.24811620.19934356451879
4.7553-5.12010.2511900.19184731492183
5.1201-5.63080.24751750.20274577475281
5.6308-6.43540.24932110.21724895510685
6.4354-8.06970.25181750.20294657483283
8.0697-26.47850.23451840.18734685486983
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)
13.31191.2709-0.39574.1722-1.50685.7024-0.13090.6787-0.2316-0.86780.41890.3146-0.0219-0.3813-0.28970.4762-0.0902-0.0560.51620.0070.524244.1193-39.58769.9573
23.52640.7022-1.68192.50770.06132.41530.04670.19660.01480.0468-0.149-0.0943-0.06630.11640.09990.16450.0315-0.00350.23220.04110.357747.5878-32.326790.1422
31.3854-0.8316-0.35110.64560.25570.1062-0.1060.3087-0.21640.1099-0.210.1360.3585-0.03480.34490.4129-0.02810.10510.3256-0.00560.43621.6452-45.755497.9378
41.4099-0.9528-0.33390.96110.43181.70140.17040.3336-0.0871-0.0143-0.1252-0.0074-0.1467-0.0383-0.00550.2572-0.07970.07250.24160.08180.326511.0302-26.0055101.0935
51.4338-1.4653-1.03621.49451.05870.74810.70070.47880.6298-0.4327-0.3931-0.1125-1.0673-0.2335-0.27510.9030.09770.42210.7651-0.08141.119917.9485-10.313590.8971
64.13472.5751-0.86151.6484-0.99254.8432-0.13860.93110.8457-1.16120.0318-0.625-0.8947-0.0194-0.610.5850.10890.10490.99950.13610.748437.6138-20.136480.7994
72.26060.6825-0.14142.9165-0.11510.72450.2564-0.7801-0.17070.9334-0.1019-0.10720.1313-0.1073-0.11571.0969-0.01290.08680.42910.17380.5472.31536.572156.2856
80.5988-0.2990.13652.1591-0.22531.0212-0.17190.01240.1970.1330.12840.1039-0.0237-0.07230.00020.50480.01140.10560.10220.12620.44773.38775.278132.2601
90.9867-0.1263-0.46280.53380.20990.8869-0.05440.07760.05980.26750.01630.12840.0734-0.06770.03390.4875-0.04340.07880.12560.09670.38111.0588-27.9812126.1697
102.0143-3.0706-0.43427.21272.04752.61340.27870.05930.63630.24020.9513-1.9560.87331.22-1.03220.96420.01660.1160.7845-0.32611.253927.2289-17.5546139.8491
117.61060.7983-2.56051.3593-1.71022.50640.1919-1.51960.8591.8318-0.50470.5402-0.7337-0.28130.33530.8446-0.12730.05160.876-0.23140.586333.2307-29.9777123.4796
125.0016-3.00720.23573.01161.60092.8034-0.681-0.3916-0.61050.32571.3008-0.32930.40391.5906-0.62740.94290.05850.31060.883-0.30471.078823.983-14.574142.037
132.8453-1.52030.81153.1157-0.86114.2127-0.3184-0.4866-0.07121.37940.19330.2418-1.0388-0.47280.18170.7960.1710.08320.46050.030.515145.24821.676341.875
144.94140.205-3.55520.54180.89464.8068-0.6069-0.3711-0.54230.31840.23470.22590.3253-0.07050.33730.77810.2166-0.00180.45510.09340.548749.9992-9.80136.9865
154.7096-1.78951.49773.27771.06822.5962-0.1067-0.0384-0.1866-0.13580.15660.209-0.02550.218-0.06360.32990.03660.07090.24630.06390.305246.3149-4.888517.4455
161.011-0.2927-0.04510.35620.19250.1329-0.0865-0.22270.7168-0.0735-0.0141-0.2007-0.0863-0.00730.14590.53370.1299-0.07240.3688-0.12250.641421.81717.424313.4814
170.64590.51730.12822.01750.95511.3683-0.0067-0.16760.061-0.0521-0.0320.1050.27290.10740.0370.41930.1186-0.01010.24550.10090.460311.0282-12.619410.3909
181.63652.8206-0.83868.8533-1.57790.43420.8952-0.1058-2.09440.7749-0.0016-0.79551.5-0.317-0.80711.046-0.0607-0.34170.6733-0.05721.305125.9351-24.073925.6319
193.42260.91580.31560.26180.4578.31730.5381-1.16950.00120.5368-0.018-0.7363-0.35330.7863-0.46581.45140.0797-0.36040.9121-0.40371.1910.6754-32.969212.2396
208.03063.80811.53425.96230.20653.7580.50130.2873-0.2479-0.7212-1.0961.279-0.1238-0.42350.67190.80830.1169-0.06360.5863-0.25560.852124.9562-19.482624.1554
212.9381-0.5614-0.74281.09620.04863.07740.00070.70990.5107-0.79120.06130.14550.36530.2695-0.10651.50880.0885-0.16790.57280.20690.6414-0.6094-43.6787-45.9874
222.1629-0.67750.30053.78570.66420.2730.01710.1097-0.2016-0.53750.07790.02320.1639-0.0258-0.07290.63630.03560.01150.15810.1130.42865.935-46.5373-24.1399
230.9965-0.19080.77410.3336-0.37320.7707-0.2559-0.3247-0.0456-0.2482-0.04810.3962-0.166-0.21530.17710.57540.1778-0.0720.32-0.0370.5724-6.4373-20.8113-17.2446
241.5543-0.06370.51960.61430.00720.8394-0.2179-0.08470.0948-0.28330.09320.0655-0.0434-0.0210.10090.67780.1240.03530.19850.1110.412313.4626-10.0916-14.1958
258.01152.12961.50745.94181.72278.08040.15380.7526-0.6398-0.95641.1077-1.23850.68050.5623-1.19731.0512-0.2186-0.16580.5380.0410.963819.5821-26.5335-30.9217
263.4789-0.9374-1.26661.7997-1.81843.4760.35120.1026-0.1720.0647-0.5354-0.5531-0.1941-0.10780.31221.18760.1846-0.52311.2638-0.57741.411434.4297-15.2826-25.9232
274.46180.8945.28970.3410.86388.84560.24920.345-0.1184-0.22480.12510.57061.1187-0.0339-0.27250.87680.0876-0.10891.0057-0.37011.139133.1714-8.5428-11.9825
287.13875.44511.59034.25931.50631.2385-0.1851-0.3860.9880.04130.16040.0964-0.41680.39250.08390.9180.0735-0.21520.7804-0.29181.220822.0167-22.499-29.3217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 115 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 247 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 248 through 289 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 290 through 437 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 27 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 36 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 3 through 144 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 145 through 263 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 264 through 437 )C0
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 12 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 13 through 19 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 20 through 35 )D0
13X-RAY DIFFRACTION13chain 'E' and (resid 3 through 106 )E0
14X-RAY DIFFRACTION14chain 'E' and (resid 107 through 144 )E0
15X-RAY DIFFRACTION15chain 'E' and (resid 145 through 247 )E0
16X-RAY DIFFRACTION16chain 'E' and (resid 248 through 289 )E0
17X-RAY DIFFRACTION17chain 'E' and (resid 290 through 437 )E0
18X-RAY DIFFRACTION18chain 'F' and (resid 1 through 9 )F0
19X-RAY DIFFRACTION19chain 'F' and (resid 10 through 19 )F0
20X-RAY DIFFRACTION20chain 'F' and (resid 20 through 35 )F0
21X-RAY DIFFRACTION21chain 'G' and (resid 2 through 115 )G0
22X-RAY DIFFRACTION22chain 'G' and (resid 116 through 247 )G0
23X-RAY DIFFRACTION23chain 'G' and (resid 248 through 289 )G0
24X-RAY DIFFRACTION24chain 'G' and (resid 290 through 437 )G0
25X-RAY DIFFRACTION25chain 'H' and (resid 1 through 6 )H0
26X-RAY DIFFRACTION26chain 'H' and (resid 7 through 12 )H0
27X-RAY DIFFRACTION27chain 'H' and (resid 13 through 19 )H0
28X-RAY DIFFRACTION28chain 'H' and (resid 20 through 35 )H0

+
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