[English] 日本語
Yorodumi
- PDB-5xox: Crystal structure of tRNA(His) guanylyltranserase from Saccharomy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xox
TitleCrystal structure of tRNA(His) guanylyltranserase from Saccharomyces cerevisiae
ComponentstRNA(His) guanylyltransferase
KeywordsTRANSFERASE / Thg1 / reverse polymerization / post-transcriptional modification / GTP
Function / homology
Function and homology information


3'-5' RNA polymerase activity / tRNAHis guanylyltransferase / tRNA guanylyltransferase activity / tRNA modification / tRNA processing / GTP binding / magnesium ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Thg1 C-terminal domain / Thg1 C terminal domain / tRNAHis guanylyltransferase Thg1 / tRNAHis guanylyltransferase catalytic domain / tRNAHis guanylyltransferase Thg1 superfamily / tRNAHis guanylyltransferase / tRNA(His) guanylyltransferase (Thg1) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / tRNA(His) guanylyltransferase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLee, K. / Lee, E.H. / Son, J. / Hwang, K.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of Korea2017R1A2B2005666 Korea, Republic Of
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure of tRNA(His) guanylyltransferase from Saccharomyces cerevisiae
Authors: Lee, K. / Lee, E.H. / Son, J. / Hwang, K.Y.
History
DepositionMay 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 16, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA(His) guanylyltransferase
B: tRNA(His) guanylyltransferase
C: tRNA(His) guanylyltransferase
D: tRNA(His) guanylyltransferase
E: tRNA(His) guanylyltransferase
F: tRNA(His) guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,05826
Polymers171,7256
Non-polymers3,33420
Water00
1
A: tRNA(His) guanylyltransferase
B: tRNA(His) guanylyltransferase
C: tRNA(His) guanylyltransferase
D: tRNA(His) guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,15020
Polymers114,4834
Non-polymers2,66716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15640 Å2
ΔGint-166 kcal/mol
Surface area41690 Å2
MethodPISA
2
E: tRNA(His) guanylyltransferase
F: tRNA(His) guanylyltransferase
hetero molecules

E: tRNA(His) guanylyltransferase
F: tRNA(His) guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,81712
Polymers114,4834
Non-polymers1,3348
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1,-y-1,z1
Buried area10640 Å2
ΔGint-118 kcal/mol
Surface area34280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.703, 164.703, 275.891
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
Components

#1: Protein
tRNA(His) guanylyltransferase / tRNA-histidine guanylyltransferase


Mass: 28620.775 Da / Num. of mol.: 6 / Fragment: UNP residues 5-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: THG1, YGR024C / Production host: Escherichia coli (E. coli) / References: UniProt: P53215, tRNAHis guanylyltransferase
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.45 Å3/Da / Density % sol: 77.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH 6.0, 0.9M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97952 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 3→29.841 Å / Num. obs: 68293 / % possible obs: 93.42 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.1419 / Net I/σ(I): 17.87
Reflection shellResolution: 3→3.107 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.3766 / Mean I/σ(I) obs: 3.02 / Num. unique obs: 12656 / % possible all: 84

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3otb

3otb


Resolution: 3→29.841 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 33.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2737 1516 2.22 %
Rwork0.2395 --
obs0.2403 68285 93.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→29.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10177 0 195 0 10372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01410627
X-RAY DIFFRACTIONf_angle_d1.72514377
X-RAY DIFFRACTIONf_dihedral_angle_d17.0686276
X-RAY DIFFRACTIONf_chiral_restr0.0731536
X-RAY DIFFRACTIONf_plane_restr0.0091775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.09680.42431300.39855408X-RAY DIFFRACTION84
3.0968-3.20730.4411260.39015583X-RAY DIFFRACTION86
3.2073-3.33560.37421290.36845662X-RAY DIFFRACTION87
3.3356-3.48720.31981340.32465841X-RAY DIFFRACTION90
3.4872-3.67070.33391320.28176009X-RAY DIFFRACTION93
3.6707-3.90020.32891330.24886131X-RAY DIFFRACTION95
3.9002-4.20060.26411440.21456391X-RAY DIFFRACTION98
4.2006-4.62190.21761470.17816455X-RAY DIFFRACTION100
4.6219-5.28750.20821400.18016482X-RAY DIFFRACTION100
5.2875-6.64960.26681510.22156494X-RAY DIFFRACTION100
6.6496-29.84250.22531500.20356313X-RAY DIFFRACTION96
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)
13.08810.21251.51811.93290.24261.0852-0.23440.71720.8037-0.18070.1593-0.0597-0.2077-0.2490.1280.30890.039-0.0640.87160.1330.8513-23.065-70.5515-43.1798
22.9654-3.95820.48626.02071.80218.48510.05761.09620.6927-1.12370.68-1.0298-0.82630.7061-0.56280.5192-0.236-0.28051.33190.47361.334-20.2236-62.653-60.4777
33.8791.2819-1.33091.9761-1.53121.8593-0.81050.64070.8031-0.12110.2737-0.3302-0.23920.25280.52790.4577-0.1504-0.17490.84130.0490.7080.0869-69.2185-44.6895
49.909-0.4752-3.83741.97152.05093.2631.11-1.69440.08040.9838-0.47250.4513-0.76090.0154-0.51220.6071-0.0406-0.15060.9809-0.1120.9813-12.376-63.0899-28.5037
58.74025.10578.34214.90534.82737.8658-0.11670.8451-0.06060.06210.0004-0.4621-0.21420.09750.24390.413-0.0475-0.05530.96860.00180.3646-17.1671-87.2574-41.2455
60.74451.28160.624.6340.83642.82150.04160.42441.0346-0.30910.00730.437-0.4871-0.85580.04510.375-0.0718-0.09311.29070.41261.165-38.5536-71.3058-55.497
72.5066-0.1621-0.24384.6272-0.031.1477-0.06090.44080.8844-0.07280.23440.3519-0.0128-0.5636-0.02540.077-0.2234-0.33791.29330.31570.6838-30.8609-76.7272-54.82
82.17751.86290.58472.21872.20954.8347-0.1061-0.23371.1775-0.1502-0.2620.8452-0.9423-1.04370.2860.5571-0.12780.00661.16770.23161.6566-35.1243-57.1174-50.4905
93.7246-0.9481-0.44431.0074-0.59670.8957-0.33710.16651.1871-0.22890.56470.7526-0.2878-0.0949-0.03880.4158-0.1748-0.25681.49090.21391.0428-48.4228-78.9185-52.0013
103.46421.0012-3.0735.0399-1.11763.5357-0.3871.11260.9977-0.02240.4123-0.1688-0.1481-0.07190.05050.5489-0.0695-0.1781.3560.20851.3727-65.748-68.9446-48.6891
112.28410.1431-0.20920.1098-0.18350.2557-0.1090.89650.50070.1615-0.23230.6622-0.24760.01420.33090.3469-0.3847-0.38852.24960.68421.6875-55.6435-71.2292-61.6806
122.09470.11820.79030.3193-0.84482.79930.46921.136-0.7326-0.51870.35830.03830.8560.2075-0.54220.5829-0.4297-0.47661.79690.52921.1855-43.0354-84.8462-66.9497
131.60241.23982.13431.81662.52827.0971-0.2839-0.4537-0.22480.57760.34110.4858-0.2973-0.4406-0.0394-0.1359-0.12190.96371.2017-0.0999-0.2953-33.7572-91.8164-28.9641
143.5746-0.59071.76793.1913-1.33644.0391-0.02020.0982-1.0458-0.19260.2578-0.03960.67050.1535-0.250.6072-0.08340.24640.7733-0.12880.7003-25.2653-119.651-36.2535
153.4801-1.56551.41263.6173-1.71262.7183-0.0545-0.0999-0.7094-0.0040.31490.3310.1326-0.0594-0.20240.469-0.11230.21890.7081-0.10920.5678-31.419-112.795-34.1732
164.6901-0.5783.14245.6537-4.22852.0059-0.17380.3209-0.95050.13370.5381-1.01780.93331.0512-0.31950.63880.11380.04610.8239-0.11221.0402-17.4854-123.7933-23.5993
172.6299-0.7031-0.4021.68120.25053.75360.01880.2796-0.6982-0.12610.4326-0.54391.80230.7157-0.15840.241-0.40670.25590.8616-0.34641.0439-19.4994-116.976-47.7447
186.68040.60012.04024.45960.02377.8155-0.42431.0706-0.3133-0.48040.2552-0.86141.16521.620.14431.26580.13240.2611.5451-0.44771.2414-3.3861-125.6152-53.2013
195.9694-2.0199-2.0965.49392.17816.73790.12711.1294-1.309-0.29440.02070.38421.1895-0.47930.07761.1863-0.49020.08681.0573-0.42360.9025-26.918-125.9083-50.2852
204.13484.01535.45814.86595.04558.0428-0.34760.1111-1.0183-0.19860.616-0.21490.67070.0399-0.20130.5063-0.08340.22381.177-0.30690.3756-20.9109-99.1461-42.6124
212.87031.92370.03492.4949-0.78292.11090.0659-0.7645-0.70110.8026-0.11650.74650.3961-0.73850.14650.67230.10720.40261.14740.21740.8249-31.119-109.6761-14.7108
223.71391.532-0.16667.7385-0.74315.2979-0.4667-0.3786-0.27140.58050.11410.2585-0.1127-0.12570.31960.44280.10120.04380.79940.01330.2602-21.3283-105.0752-21.1253
234.39194.28480.01299.7644-0.96312.3421-0.4419-0.3619-0.6226-0.11170.08570.76290.6378-0.48170.25650.6969-0.03470.32430.86370.15630.5677-31.8538-110.5452-20.6614
249.63293.291-8.41162.4909-3.35557.8002-0.4741-0.3022-0.75630.51670.23610.89590.0744-0.30780.07950.64450.28730.26081.40480.22950.8612-36.8823-97.5716-7.3589
250.3883-0.4210.10480.4513-0.10650.02620.08820.8575-0.5180.13280.23131.8694-0.0209-1.9756-0.24550.97640.1080.65882.60990.0071.907-54.8711-101.474-4.2518
268.1254-4.81934.81434.71110.67432.0074-0.7628-1.0660.21320.8760.59430.61940.1188-0.92360.1371.46320.16570.68371.67430.04490.9162-45.4887-96.35274.2442
275.7193-1.4245-7.56510.37571.88232.00520.0123-2.0944-0.1061.35080.43450.81170.76690.39-0.2021.62890.06680.46661.38540.09520.8811-30.0072-102.3553-1.0511
283.9732-1.7171-1.51710.88121.09531.97050.8222-0.8222-0.05390.1273-0.173-0.4638-0.62491.3209-0.55181.31250.21940.04891.4289-0.09580.595-17.636-95.8738-6.6599
296.1799-2.5333-0.89092.7981-1.18061.5641-0.7756-0.73390.34360.1208-0.007-0.024-0.2679-0.27380.71140.58730.1677-0.08612.0744-0.12191.1204-81.8106-82.3509-39.2559
305.72980.4061-1.35263.50340.14911.2326-0.2058-1.29270.29560.42380.2333-0.51220.0554-0.012-0.05890.49010.25080.1812.56190.35631.2812-70.069-88.8583-21.4328
311.238-2.1967-1.07314.12971.20553.235-0.1149-0.3126-0.3986-0.04290.1930.7931-0.0894-0.2304-0.00870.38070.31590.35682.59350.42611.0539-74.2984-95.9876-32.5082
324.4424-0.0260.26721.36580.36591.8958-0.7508-1.319-0.668-0.01920.55830.54420.6461-0.13550.5586-1.04510.5060.81762.57680.30181.076-80.0958-90.3482-32.1278
333.1285-0.1798-0.42051.43650.43892.5097-0.5815-1.70410.02640.40240.2482-0.19650.00270.12160.31810.6560.21050.00862.2847-0.00531.2207-74.4769-81.8441-27.354
346.14530.86343.69922.4534-0.0052.4373-0.9736-1.224-0.55331.05580.38650.79210.25840.03190.5950.88970.17570.31832.26540.25681.1268-57.5878-88.9685-33.0678
354.08770.6924-2.35227.50147.04232.0065-0.8421-1.07661.0791-0.1077-0.00950.4211-0.2234-0.15490.82890.82960.3901-0.10861.81540.09661.0128-44.7684-76.9809-28.0302
362.6796-0.0883-0.3826-0.00790.02390.0339-0.1503-1.2574-0.790.45610.32350.3005-0.1753-0.0137-0.13950.63770.65060.4252.7380.39411.4783-50.5504-92.2124-25.0519
377.9590.6444-0.56031.0246-1.02431.03310.6461.0261-2.8382-0.03690.19580.55010.4788-0.4749-0.5670.98180.40040.51291.89370.28682.1916-66.9944-104.7014-33.1699
380.75850.24860.46626.60241.51940.5743-0.0366-0.20990.06280.0719-0.04720.0767-0.0478-0.05410.05860.46830.0434-0.14651.86620.74981.5903-78.2682-66.101-56.952
391.8859-4.38061.18661.9998-2.29311.358-0.51332.090.6478-0.31830.5903-0.0564-0.16030.6771-0.16310.463-0.24050.10522.3609-0.13291.1335-74.5666-84.3581-56.8051
402.53380.9284-1.32912.99321.00511.52210.1440.0167-0.0439-0.2528-0.26860.32150.07490.30830.00450.20570.1392-0.06571.9916-0.65141.0557-86.4718-91.869-71.4525
412.4559-3.5019-0.30524.98360.4350.036-0.2603-0.1449-0.1665-0.49830.17230.0298-0.17790.82470.1090.9512-0.21220.16641.9219-0.56431.3718-96.6703-92.0323-86.248
422.00176.57162.49578.84922.2021.02320.3090.0232-0.1894-0.2655-0.4758-1.04290.33480.22950.05280.7292-0.36410.34142.124-0.16550.947-76.6703-93.6307-78.8842
437.45038.24440.88899.11110.98690.1046-1.42110.05830.0045-2.22370.7928-2.2253-1.81351.27050.51690.92250.080.63742.0674-0.08941.3433-66.8329-94.8876-70.1415
449.4742.91663.97463.5343-2.01275.6140.3085-0.42480.513-0.15890.37620.0236-0.36770.6932-0.57780.6250.17670.14732.0429-0.04681.2108-68.4553-89.9643-63.8643
452.2761-0.5958-0.35862.0135-0.71190.3746-0.2333-0.77770.780.0238-0.0156-0.65550.21640.5582-0.21760.3968-0.11670.57142.316-0.36831.1793-77.7784-84.6844-70.0523
461.99881.99851.99951.99881.99992.00050.1293-0.5117-0.82660.2999-0.0017-0.26431.04870.0964-0.08020.8286-0.06250.38521.7038-0.26720.7059-78.0428-97.3054-57.4122
471.928-3.08731.64374.9288-2.62561.3980.0873-0.45270.00550.44770.163-0.2997-0.13390.0944-0.07420.8985-0.24520.73041.6597-0.44431.3936-78.855-104.5966-60.985
480.0453-0.0603-0.09940.06130.13330.22920.03590.2823-0.2985-0.33330.0661-0.06540.2673-0.1041-0.21150.55840.24120.41461.7534-0.54951.751-88.2227-106.3201-68.7234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 116 )
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 129 )
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 215 )
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 233 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 22 )
6X-RAY DIFFRACTION6chain 'B' and (resid 23 through 74 )
7X-RAY DIFFRACTION7chain 'B' and (resid 75 through 116 )
8X-RAY DIFFRACTION8chain 'B' and (resid 117 through 129 )
9X-RAY DIFFRACTION9chain 'B' and (resid 130 through 169 )
10X-RAY DIFFRACTION10chain 'B' and (resid 170 through 195 )
11X-RAY DIFFRACTION11chain 'B' and (resid 196 through 216 )
12X-RAY DIFFRACTION12chain 'B' and (resid 217 through 233 )
13X-RAY DIFFRACTION13chain 'C' and (resid 5 through 22 )
14X-RAY DIFFRACTION14chain 'C' and (resid 23 through 74 )
15X-RAY DIFFRACTION15chain 'C' and (resid 75 through 116 )
16X-RAY DIFFRACTION16chain 'C' and (resid 117 through 129 )
17X-RAY DIFFRACTION17chain 'C' and (resid 130 through 171 )
18X-RAY DIFFRACTION18chain 'C' and (resid 172 through 195 )
19X-RAY DIFFRACTION19chain 'C' and (resid 196 through 233 )
20X-RAY DIFFRACTION20chain 'D' and (resid 5 through 22 )
21X-RAY DIFFRACTION21chain 'D' and (resid 23 through 64 )
22X-RAY DIFFRACTION22chain 'D' and (resid 65 through 116 )
23X-RAY DIFFRACTION23chain 'D' and (resid 117 through 139 )
24X-RAY DIFFRACTION24chain 'D' and (resid 140 through 171 )
25X-RAY DIFFRACTION25chain 'D' and (resid 172 through 182 )
26X-RAY DIFFRACTION26chain 'D' and (resid 183 through 201 )
27X-RAY DIFFRACTION27chain 'D' and (resid 202 through 216 )
28X-RAY DIFFRACTION28chain 'D' and (resid 217 through 233 )
29X-RAY DIFFRACTION29chain 'E' and (resid 5 through 39 )
30X-RAY DIFFRACTION30chain 'E' and (resid 40 through 64 )
31X-RAY DIFFRACTION31chain 'E' and (resid 65 through 77 )
32X-RAY DIFFRACTION32chain 'E' and (resid 78 through 116 )
33X-RAY DIFFRACTION33chain 'E' and (resid 117 through 139 )
34X-RAY DIFFRACTION34chain 'E' and (resid 140 through 169 )
35X-RAY DIFFRACTION35chain 'E' and (resid 170 through 186 )
36X-RAY DIFFRACTION36chain 'E' and (resid 187 through 216 )
37X-RAY DIFFRACTION37chain 'E' and (resid 217 through 233 )
38X-RAY DIFFRACTION38chain 'F' and (resid 9 through 12 )
39X-RAY DIFFRACTION39chain 'F' and (resid 13 through 22 )
40X-RAY DIFFRACTION40chain 'F' and (resid 23 through 36 )
41X-RAY DIFFRACTION41chain 'F' and (resid 37 through 41 )
42X-RAY DIFFRACTION42chain 'F' and (resid 42 through 65 )
43X-RAY DIFFRACTION43chain 'F' and (resid 66 through 70 )
44X-RAY DIFFRACTION44chain 'F' and (resid 83 through 91 )
45X-RAY DIFFRACTION45chain 'F' and (resid 92 through 134 )
46X-RAY DIFFRACTION46chain 'F' and (resid 135 through 139 )
47X-RAY DIFFRACTION47chain 'F' and (resid 140 through 148 )
48X-RAY DIFFRACTION48chain 'F' and (resid 149 through 154 )

+
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