[English] 日本語
Yorodumi
- PDB-4jkr: Crystal Structure of E. coli RNA Polymerase in complex with ppGpp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jkr
TitleCrystal Structure of E. coli RNA Polymerase in complex with ppGpp
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA polymerase sigma factor RpoD
KeywordsTRANSCRIPTION / transferase / RNA polymerase / transcription regulation
Function / homology
Function and homology information


sigma factor antagonist complex / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / negative regulation of DNA-templated transcription ...sigma factor antagonist complex / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / negative regulation of DNA-templated transcription / DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 ...RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / STRONTIUM ION / DNA-directed RNA polymerase subunit beta / : / : / : / : / RNA polymerase sigma factor RpoD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsZuo, Y. / Wang, Y. / Steitz, T.A.
CitationJournal: Mol.Cell / Year: 2013
Title: The mechanism of E. coli RNA polymerase regulation by ppGpp is suggested by the structure of their complex.
Authors: Zuo, Y. / Wang, Y. / Steitz, T.A.
History
DepositionMar 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoD
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)927,76926
Polymers925,60012
Non-polymers2,16914
Water00
1
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)464,06015
Polymers462,8006
Non-polymers1,2609
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42630 Å2
ΔGint-319 kcal/mol
Surface area167580 Å2
MethodPISA
2
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)463,70911
Polymers462,8006
Non-polymers9095
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41220 Å2
ΔGint-246 kcal/mol
Surface area170520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.575, 206.164, 311.062
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.423137, -0.006192, 0.906044), (0.06276, -0.997775, 0.022491), (0.903889, 0.06638, 0.422584)-67.48786, 221.84384, 36.36831
3given(-0.443194, 0.001027, 0.896425), (0.044547, -0.998739, 0.023168), (0.895318, 0.050201, 0.442589)-69.83331, 219.64449, 37.17186
4given(0.953395, -0.294807, -0.064243), (0.299596, 0.899711, 0.317431), (-0.035781, -0.321884, 0.946103)124.17278, 5.55655, -14.73211

-
Components

-
DNA-directed RNA polymerase subunit ... , 4 types, 10 molecules ABGHCIDJEK

#1: Protein
DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 36558.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / DH10B / Gene: ECDH10B_3470, O3O_23125, rpoA / Production host: Escherichia coli (E. coli) / References: UniProt: K0BPQ3, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 150820.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 2011C-3493 / Gene: ECDH1ME8569_3846, EcDH1_4008, O3K_23925, rpoB / Production host: Escherichia coli (E. coli)
References: UniProt: C9QV90, UniProt: A0A0E0Y7A2*PLUS, DNA-directed RNA polymerase
#3: Protein DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA' / RNAP SUBUNIT BETA' / RNA POLYMERASE SUBUNIT BETA' / TRANSCRIPTASE SUBUNIT BETA'


Mass: 156537.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 2009EL-2071 / Gene: BWG_3647, O3O_01425, rpoC / Production host: Escherichia coli (E. coli) / References: UniProt: C5A0S8, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 10118.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 2009EL-2071 / Gene: ECDH1ME8569_3534, EcDH1_0056, O3O_25075, rpoZ / Production host: Escherichia coli (E. coli) / References: UniProt: C9QUL2, DNA-directed RNA polymerase

-
Protein , 1 types, 2 molecules FL

#5: Protein RNA polymerase sigma factor RpoD / Sigma-70


Mass: 72206.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: alt, b3067, JW3039, rpoD / Production host: Escherichia coli (E. coli) / References: UniProt: P00579

-
Non-polymers , 3 types, 14 molecules

#6: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Sr
#7: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N5O17P4
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG400, 0.18M strontium chloride, 0.1M HEPES , pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 4.2→39.97 Å / Num. all: 88437 / Num. obs: 88171 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 %

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.2→39.97 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: THROUGHOUT / ESU R Free: 1.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31802 4396 5 %RANDOM
Rwork0.24663 ---
obs0.25027 83775 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 280.907 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2--0.67 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 4.2→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58242 0 84 0 58326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01959183
X-RAY DIFFRACTIONr_angle_refined_deg0.9351.9879894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.94457392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23824.1262785
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8011511015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.24915546
X-RAY DIFFRACTIONr_chiral_restr0.0570.29089
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02144252
LS refinement shellResolution: 4.2→4.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 308 -
Rwork0.393 6077 -
obs--99.95 %
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)
19.1083-0.6881-0.73296.95333.05034.9597-0.0771.25610.0342-1.61830.18950.1146-0.6029-0.2769-0.11240.6372-0.0405-0.18080.73110.23770.2562-2.10690.986-45.739
26.9972-1.6781.90345.52080.81784.8752-0.1073-0.00010.0149-0.51080.0880.43280.7267-0.21950.01920.28460.0698-0.09230.608-0.02550.24898.49660.651-33.784
37.7098-4.1668-1.188412.86462.813612.4113-0.1105-0.3054-0.9485-0.1392-0.5752.1373-0.2389-0.95810.68540.2306-0.015-0.13640.9755-0.05721.047-18.38192.811-31.959
45.8745-2.78320.4377.70392.56713.1920.48910.59480.525-1.99860.24270.6936-0.2985-0.14-0.73171.42580.263-0.27160.97940.67781.5946-22.501125.374-39.386
52.1583-0.33880.15181.8406-0.39141.37350.0610.06840.3508-0.2116-0.0669-0.2892-0.37330.28210.00590.2352-0.1420.01970.59010.1040.419120.93692.984-11.285
62.31510.7402-0.25013.30291.60332.65590.1091-0.0840.55070.1692-0.13750.6276-0.1736-0.31750.02850.16650.08570.06530.58390.02630.7494-16.36191.70314.673
76.39440.1982-2.22392.7121-0.07362.8924-0.51340.1825-1.46110.14150.154-0.6670.20740.06020.35950.07770.0727-0.04020.6545-0.16771.178221.01444.409-12.133
811.63753.3773-0.63269.4461.52353.984-0.32660.1367-0.9205-0.0783-0.1558-0.10530.7411-0.09470.48240.5044-0.1384-0.0081.0484-0.08921.1173-33.92143.1462.764
92.3975-1.7572.25474.4796-3.25187.56070.0802-0.1772-0.65720.9498-0.2963-0.06730.6270.92930.21620.65570.21370.10260.89950.27220.788136.66852.59916.74
102.94160.72241.29397.0802-0.22235.761-0.2572-0.09320.16631.52790.3318-0.0833-0.2482-0.1695-0.07450.48640.2081-0.17790.98290.09450.603740.69680.85938.741
119.4845-0.3023-3.17785.4398-1.91482.0126-0.2995-0.13222.53220.98130.7549-2.08310.2929-0.0371-0.45542.69320.0507-1.54380.7719-0.57972.047656.835101.53758.56
121.66574.05492.11919.59556.76882.9704-0.7243-1.08941.33290.8076-0.49050.084-0.565-0.91521.21471.7789-0.075-1.70992.916-1.0022.39188.723121.6748.423
131.40611.31810.36962.5626-1.64044.4607-0.5411-0.7087-0.1564-1.21670.277-0.43360.2003-0.61720.26411.3677-0.33930.46362.1110.25573.167323.283129.99234.74
141.5392-0.27840.68711.7688-0.06382.74090.205-0.0642-0.30590.4327-0.0841-0.17420.7266-0.1091-0.12090.6495-0.067-0.15790.58480.05620.7251-1.6650.46252.396
155.52070.1662-3.83512.05052.77417.7938-0.50470.87360.3747-1.05740.27031.95570.4508-1.21290.23440.47670.0076-0.73631.09950.11061.3686-110.272124.23721.627
162.0407-2.1225-0.23558.92430.83128.5223-0.0110.51680.6089-0.65830.08111.1184-0.26140.1327-0.07020.44710.0676-0.43930.9370.37581.5663-105.439155.29535.07
177.9837-0.69281.490812.14199.95448.75710.2011.75550.0519-1.0530.1946-0.4402-0.71640.4129-0.39561.2005-0.2324-0.65531.11230.1750.8651-90.921122.96212.411
1814.483-8.6294-2.38098.46293.28622.74430.07721.4902-2.0187-0.4926-0.4472.3182-0.3581-0.31610.36991.5979-0.2161-0.80841.1161-0.46171.7298-93.09389.9236.768
191.28380.2464-0.17432.73311.49253.25720.1528-0.0383-0.07380.13950.12060.6980.5273-0.2439-0.27350.3906-0.0627-0.18010.46660.1830.7982-88.61124.77957.063
203.8025-1.30330.3433.0816-0.7412.0533-0.03960.6511-0.344-0.83330.0179-0.42820.37940.27940.02160.68030.0416-0.12060.7639-0.11910.6988-49.648127.62234.109
211.24780.204-0.40081.96420.00952.3271-0.0215-0.31080.5972-0.3963-0.10010.8111-0.5776-0.66080.12161.08550.2619-0.32081.08160.19881.4128-92.51173.04355.67
226.6053-1.44061.42628.0963-1.94813.7953-0.16650.1790.8889-0.66970.5881-0.438-0.5519-0.2-0.42161.4702-0.11780.11220.79820.1770.5311-52.538176.21212.541
235.06132.92444.02784.38943.18964.9047-0.0103-0.26240.42180.8147-0.2945-0.0434-0.74690.1460.30481.50540.0202-0.17730.36920.11410.928-73.01166.74283.238
245.23520.9912.81774.61750.04332.3485-0.16150.6486-0.28140.19120.39-0.2095-0.13690.3899-0.22860.76710.13070.04340.7564-0.19190.3021-52.198139.57395.31
2512.29985.51040.170812.8845-4.430710.1001-0.393-0.4451-2.14760.52710.083-1.1004-0.02330.10750.30990.86630.3182-0.31660.6066-0.20691.0358-40.652118.621117.891
2611.7324-8.16824.152414.8147-6.2052.73530.8304-0.51060.7955-0.8803-0.9931-0.92510.62520.23950.16271.88760.6587-0.57762.36820.29651.1928-28.39699.8372.61
272.7395-0.8452.42090.4959-1.41144.04560.2332-1.0983-0.3135-0.49530.04560.07761.4250.0355-0.27882.30160.2592-0.03331.9772-0.00752.5829-46.36890.35780.944
282.28880.55610.60722.06730.11532.0558-0.34160.28010.36630.00070.0804-0.0066-0.56420.1020.26130.849-0.0316-0.26560.6086-0.08340.571-23.481170.12363.507
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 51
2X-RAY DIFFRACTION1A179 - 232
3X-RAY DIFFRACTION1A401
4X-RAY DIFFRACTION2A52 - 178
5X-RAY DIFFRACTION3B6 - 51
6X-RAY DIFFRACTION3B179 - 232
7X-RAY DIFFRACTION4B52 - 178
8X-RAY DIFFRACTION5C3 - 28
9X-RAY DIFFRACTION5C146 - 152
10X-RAY DIFFRACTION5C445 - 455
11X-RAY DIFFRACTION5C517 - 831
12X-RAY DIFFRACTION5C1057 - 1241
13X-RAY DIFFRACTION5C1402
14X-RAY DIFFRACTION5D501 - 790
15X-RAY DIFFRACTION6C1242 - 1320
16X-RAY DIFFRACTION6D343 - 500
17X-RAY DIFFRACTION6D791 - 930
18X-RAY DIFFRACTION6D1136 - 1153
19X-RAY DIFFRACTION6D1213 - 1317
20X-RAY DIFFRACTION6D1345 - 1376
21X-RAY DIFFRACTION6C1401
22X-RAY DIFFRACTION6D2003 - 2004
23X-RAY DIFFRACTION6E2 - 91
24X-RAY DIFFRACTION6D2001
25X-RAY DIFFRACTION6E101
26X-RAY DIFFRACTION6F520 - 529
27X-RAY DIFFRACTION7C832 - 891
28X-RAY DIFFRACTION7C912 - 1056
29X-RAY DIFFRACTION8C892 - 911
30X-RAY DIFFRACTION8F530 - 613
31X-RAY DIFFRACTION8F701
32X-RAY DIFFRACTION9C29 - 145
33X-RAY DIFFRACTION9C456 - 516
34X-RAY DIFFRACTION10C153 - 225
35X-RAY DIFFRACTION10C338 - 444
36X-RAY DIFFRACTION11C226 - 337
37X-RAY DIFFRACTION12D1154 - 1212
38X-RAY DIFFRACTION13D947 - 1126
39X-RAY DIFFRACTION14C1321 - 1342
40X-RAY DIFFRACTION14D10 - 342
41X-RAY DIFFRACTION14D1318 - 1344
42X-RAY DIFFRACTION14D2002
43X-RAY DIFFRACTION14F95 - 519
44X-RAY DIFFRACTION15G6 - 51
45X-RAY DIFFRACTION15G179 - 232
46X-RAY DIFFRACTION16G52 - 178
47X-RAY DIFFRACTION17H6 - 51
48X-RAY DIFFRACTION17H179 - 232
49X-RAY DIFFRACTION18H52 - 178
50X-RAY DIFFRACTION19I3 - 28
51X-RAY DIFFRACTION19I146 - 152
52X-RAY DIFFRACTION19I445 - 455
53X-RAY DIFFRACTION19I517 - 831
54X-RAY DIFFRACTION19I1057 - 1241
55X-RAY DIFFRACTION19J501 - 790
56X-RAY DIFFRACTION20I1242 - 1320
57X-RAY DIFFRACTION20J343 - 500
58X-RAY DIFFRACTION20J791 - 930
59X-RAY DIFFRACTION20J1136 - 1153
60X-RAY DIFFRACTION20J1213 - 1317
61X-RAY DIFFRACTION20J1345 - 1376
62X-RAY DIFFRACTION20I1401
63X-RAY DIFFRACTION20J1502 - 1503
64X-RAY DIFFRACTION20K2 - 91
65X-RAY DIFFRACTION20K101
66X-RAY DIFFRACTION20L520 - 529
67X-RAY DIFFRACTION21I832 - 891
68X-RAY DIFFRACTION21I912 - 1056
69X-RAY DIFFRACTION22I892 - 911
70X-RAY DIFFRACTION22L530 - 613
71X-RAY DIFFRACTION23I29 - 145
72X-RAY DIFFRACTION23I456 - 516
73X-RAY DIFFRACTION24I153 - 225
74X-RAY DIFFRACTION24I338 - 444
75X-RAY DIFFRACTION25I226 - 337
76X-RAY DIFFRACTION26J1154 - 1212
77X-RAY DIFFRACTION27J947 - 1126
78X-RAY DIFFRACTION28I1321 - 1342
79X-RAY DIFFRACTION28J14 - 342
80X-RAY DIFFRACTION28J1318 - 1344
81X-RAY DIFFRACTION28J1501
82X-RAY DIFFRACTION28L95 - 519

+
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