[English] 日本語
Yorodumi
- PDB-4yfn: Escherichia coli RNA polymerase in complex with squaramide compou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yfn
TitleEscherichia coli RNA polymerase in complex with squaramide compound 14 (N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide)
Components
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA polymerase sigma factor RpoD
Keywordstranscription/transcription inhibitor / switch region / squaramide / transcription-transcription inhibitor complex
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-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat ...sigma factor antagonist complex / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein dimerization activity / negative regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #1670 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region ...Helix Hairpins - #1670 / RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / 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 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / 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 / Helix Hairpins / 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 / Gyrase A; domain 2 / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / 5' to 3' exonuclease, C-terminal subdomain / Beta Complex / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like 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 / Special / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Roll / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-4C2 / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit beta' / RNA polymerase sigma factor RpoD
Similarity search - Component
Biological speciesEscherichia coli O139:H28 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.817 Å
AuthorsMolodtsov, V. / Fleming, P.R. / Eyermann, C.J. / Ferguson, A.D. / Foulk, M.A. / McKinney, D.C. / Masse, C.E. / Buurman, E.T. / Murakami, K.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087350 United States
CitationJournal: J.Med.Chem. / Year: 2015
Title: X-ray Crystal Structures of Escherichia coli RNA Polymerase with Switch Region Binding Inhibitors Enable Rational Design of Squaramides with an Improved Fraction Unbound to Human Plasma Protein.
Authors: Molodtsov, V. / Fleming, P.R. / Eyermann, C.J. / Ferguson, A.D. / Foulk, M.A. / McKinney, D.C. / Masse, C.E. / Buurman, E.T. / Murakami, K.S.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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
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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _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
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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)921,14920
Polymers919,81412
Non-polymers1,3358
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)460,57410
Polymers459,9076
Non-polymers6684
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37610 Å2
ΔGint-186 kcal/mol
Surface area161770 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)460,57410
Polymers459,9076
Non-polymers6684
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36690 Å2
ΔGint-173 kcal/mol
Surface area156510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.247, 206.569, 312.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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 O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / Gene: rpoA, EcE24377A_3778 / Plasmid: pGEMABC / Details (production host): addgene #45398 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: A7ZSI4, 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 O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / Gene: rpoB, EcE24377A_4528 / Plasmid: pGEMABC / Details (production host): addgene #45398 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: A7ZUK1, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 155366.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / Gene: rpoC, EcE24377A_4529 / Plasmid: pGEMABC / Details (production host): addgene #45398 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: A7ZUK2, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 10249.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O139:H28 (strain E24377A / ETEC) (bacteria)
Strain: E24377A / ETEC / Gene: rpoZ, EcE24377A_4152 / Plasmid: pACYCDuet-1_Ec_rpoZ / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: A7ZTK1, DNA-directed RNA polymerase

-
Protein , 1 types, 2 molecules FL

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


Mass: 70352.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rpoD, alt, b3067, JW3039 / Plasmid: pGEMD / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: P00579

-
Non-polymers , 3 types, 8 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-4C2 / N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide


Mass: 512.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23F3N4O5S

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES-HCL (PH7), 0.2M CaACETATE, 15% PEG400 / PH range: 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 3.8→30 Å / Num. obs: 107176 / % possible obs: 89.7 % / Redundancy: 6.6 % / Net I/σ(I): 15.8

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IGC

4igc
PDB Unreleased entry


Resolution: 3.817→29.963 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 2000 1.87 %
Rwork0.2215 --
obs0.2224 104940 88.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.817→29.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55562 0 76 0 55638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01856447
X-RAY DIFFRACTIONf_angle_d1.82176199
X-RAY DIFFRACTIONf_dihedral_angle_d19.94921790
X-RAY DIFFRACTIONf_chiral_restr0.0848684
X-RAY DIFFRACTIONf_plane_restr0.0099980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8167-3.9120.36441300.3446466X-RAY DIFFRACTION77
3.912-4.01750.36911320.33647003X-RAY DIFFRACTION84
4.0175-4.13540.39771410.32017048X-RAY DIFFRACTION84
4.1354-4.26860.29961270.2947040X-RAY DIFFRACTION84
4.2686-4.42070.33911460.27847065X-RAY DIFFRACTION85
4.4207-4.59710.29181370.26637001X-RAY DIFFRACTION84
4.5971-4.80550.3171240.24857057X-RAY DIFFRACTION84
4.8055-5.05770.26041290.2387001X-RAY DIFFRACTION83
5.0577-5.37290.29011480.23727292X-RAY DIFFRACTION87
5.3729-5.7850.28241410.22817824X-RAY DIFFRACTION93
5.785-6.36210.28511560.23918315X-RAY DIFFRACTION98
6.3621-7.27120.2931590.22888489X-RAY DIFFRACTION100
7.2712-9.11790.2281630.18168560X-RAY DIFFRACTION100
9.1179-29.96420.21731670.16868737X-RAY DIFFRACTION99
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)
10.1619-0.3728-0.19680.03780.84230.1603-0.036-0.86460.45860.2099-0.0087-0.1662-0.7946-0.166701.9552-0.0874-0.07182.31450.10061.9626-90.853-9.29747.501
20.44110.42510.60021.9232-0.08060.93820.0668-0.2311-0.29980.2073-0.0663-0.3990.35220.115201.8866-0.14-0.10462.13680.26141.8092-103.66-42.20334.678
30.34-0.06050.17550.2681-0.16380.4590.0541-0.48990.06311.3676-0.1941-0.2309-0.5483-0.320502.3205-0.0118-0.22972.27120.01991.7819-92.367-12.3745.733
40.0141-0.00110.0448-0.0036-0.00950.18570.0855-0.0232-0.0508-0.04310.0719-0.03910.01250.1516-0.00031.85080.1226-0.45782.2370.45642.1137-65.755-13.16135.126
50.479-0.00070.12250.11240.12090.2235-0.4933-0.9071-0.0836-0.65590.2208-0.75380.04220.401401.8301-0.25130.06752.06960.01261.9544-77.206-11.730.793
60.47620.28990.14780.277-0.24620.29190.0909-0.3370.0640.4286-0.14560.02-0.85140.209602.75-0.4735-0.46852.4613-0.21052.3245-71.42822.29637.93
70.3308-0.55150.09380.1896-0.34750.40290.0099-0.2848-0.25250.0855-0.2347-1.2363-0.01740.665601.9389-0.2425-0.27932.1220.05112.0874-77.024-9.39133.175
82.12410.77090.38451.3401-0.02180.73740.080.1997-0.3760.1751-0.09910.53020.4197-0.333901.5136-0.12750.09222.0003-0.0131.7776-134.755-44.092-8.851
91.00671.41540.03321.0991-0.25430.9434-0.1350.11311.0338-0.863-0.12790.5364-0.58560.062702.59420.0195-0.35572.2895-0.13132.3233-145.277-10.371-49.527
100.33330.68440.87780.7785-0.61770.4303-0.11070.33030.0456-0.53360.07650.2688-0.17620.0201-01.7868-0.0984-0.00222.2182-0.03031.8656-137.395-31.612-29.729
110.82271.26511.17212.07140.76242.0234-0.04570.15570.1036-0.0872-0.13580.4115-0.3526-0.501-01.20980.02230.09551.9537-0.02581.7164-130.677-21.515-3.017
121.1170.2816-0.25841.94720.87041.84790.025-0.2775-0.3940.5425-0.0565-0.04750.4936-0.190101.4335-0.1626-0.00841.84310.12241.5637-113.694-39.77715.615
130.14670.1192-0.26311.0003-0.03130.9707-0.01030.0936-0.52490.1614-0.07880.16170.3321-0.1731-01.9203-0.1363-0.03672.09530.11882.0531-118.965-60.90713.947
141.4415-0.4259-0.48621.77110.41541.39150.1089-0.4281-0.00380.3893-0.09230.265-0.1143-0.178-01.2746-0.0669-0.00441.8614-0.02031.5414-113.638-18.72821.528
150.6868-0.31621.761.00530.76960.74240.19890.067-0.3439-0.1582-0.2066-0.39880.33280.6765-01.31120.02280.06181.82670.16651.7742-80.322-30.219-17.897
162.28530.32961.50612.2179-0.07583.20050.0520.35780.0602-0.3372-0.0106-0.06260.00350.1692-01.51590.06890.0931.8462-0.03521.6967-90.899-39.648-45.923
171.1355-0.1532-0.3941.19310.12721.0320.18060.29340.443-0.2842-0.2049-0.1207-0.472-0.008701.4715-0.0558-0.10081.7790.10421.829-92.4790.032-10.541
180.16090.1596-0.04620.06770.0529-0.0227-0.2928-0.62330.1943-0.36550.4538-0.7905-0.38280.8009-02.33530.1192-0.03222.25260.09932.4925-62.318-13.674-2.592
19-0.11-0.2868-0.0074-0.0954-0.0932-0.05170.713-0.3960.4107-0.4466-0.03410.10590.52290.918302.41380.202-0.26642.4441-0.02712.6375-43.202-24.176-16.73
20-0.5883-0.2899-0.93590.41540.1030.1106-0.2015-0.3572-0.2536-0.33730.06810.10570.56140.19402.97090.2219-0.39422.6544-0.17642.7377-98.305-76.166-67.181
21-0.1360.2731-0.0736-0.04220.093-0.29880.40670.17530.7172-1.4172-0.0226-0.58620.28040.3448-03.8553-0.12220.793.1479-0.24963.7727-76.98-60.895-83.586
221.12920.18151.0731.9046-0.13271.50810.1707-0.168-0.2964-0.4786-0.10690.41050.8767-0.410102.0206-0.1235-0.15232.12670.16212.2304-108.149-60.557-39.204
230.44640.4522-0.05740.3657-0.1848-0.2567-0.0393-0.4445-0.74670.4-0.1157-0.24320.47890.177-02.22440.0413-0.00162.28050.28312.5308-59.139-60.422-3.295
240.01590.1941-0.063-0.02250.0227-0.04960.3606-0.2802-0.1455-1.2386-0.8274-0.08870.60840.029702.75910.4235-0.4642.6053-0.31022.707516.17218.788-21.009
250.3276-0.1830.56650.6088-0.2750.3606-0.0603-0.373-0.19640.42910.1415-0.2358-0.45050.2578-02.33270.1561-0.59092.3066-0.35792.917710.98551.367-34.195
26-0.02260.03590.0091-0.18960.0149-0.0454-0.24970.0186-0.2823-0.5483-0.297-0.45810.0538-0.048703.26650.4833-0.7282.4306-0.18682.855414.62221.118-20.25
27-0.0480.18160.23080.0372-0.23160.07650.1979-0.44250.3010.25690.24932.27220.55390.328303.18730.383-0.32272.3304-0.03712.7657-5.32221.415-12.328
280.1045-0.2644-0.22380.11450.14380.1094-0.4884-0.33090.205-0.41610.3378-0.09110.28050.291703.92670.4979-0.50362.47070.26482.827-4.345-12.81-5.01
290.35340.2612-0.2723-0.1629-0.12160.26680.46250.1876-0.2710.3224-0.06830.5020.73660.946303.49520.4057-0.52732.57480.07822.361-3.62719.014-11.396
301.4984-0.2745-0.07020.70660.56422.23030.01620.37490.3447-0.4841-0.0247-0.5852-0.3510.1232-02.0804-0.0359-0.06441.93870.04242.3786-14.43555.79-81.365
312.59190.0040.7241.3204-0.2791.1539-0.0230.1051-0.41280.15730.04170.40140.5604-0.3909-02.1959-0.07290.0632.05130.13931.926-50.55523.806-106.487
320.89441.12010.92290.8134-0.07110.7988-0.12330.08610.2435-0.16530.0401-0.1734-0.21-0.168702.0882-0.00230.00812.04740.04031.9509-33.61944.634-92.556
330.79780.1950.70471.7049-0.3921.5590.1440.1977-0.0993-0.03760.0645-0.35970.49990.160702.11760.1472-0.15151.8801-0.12742.1899-13.00433.157-75.202
341.4338-0.39890.08251.1982-0.451.78140.0837-0.14780.29240.20160.2658-0.477500.417102.21850.1061-0.28751.9692-0.15672.3203-2.31250.25-51.458
350.13790.21240.5791.8743-0.71720.4774-0.19540.775-0.1853-0.72750.0469-0.64520.20180.2856-02.6193-0.0269-0.00022.7129-0.2122.6914-0.31471.603-56.562
360.36220.535-0.39090.98920.26311.6136-0.1743-0.1685-0.1770.28120.3502-0.79250.45910.6604-02.33950.3274-0.5292.1534-0.14542.42051.4828.809-49.242
370.2694-0.42280.47470.9473-0.09380.7053-0.1089-0.57480.32630.68680.2783-0.11710.2647-0.395802.4919-0.1606-0.19631.8874-0.02371.9524-47.83244.015-36.04
381.8043-0.13040.91121.5539-0.09172.3659-0.0474-0.2026-0.01620.1107-0.14130.12150.1797-0.4067-02.031-0.06960.07691.97140.0831.8193-67.76954.709-58.636
391.0967-0.4993-0.53980.77590.31260.9804-0.21110.0295-0.49170.66780.08180.03810.8651-0.310503.0093-0.166-0.16071.86970.10372.075-38.04212.88-43.983
40-0.11590.04830.0545-0.07570.0285-0.1282-0.8449-0.70130.5747-0.24560.54420.81050.9518-1.0584-04.29040.0201-0.18823.15050.29673.2085-42.30927.126-13.683
41-0.1220.0096-0.12920.0069-0.0388-0.01640.24670.00230.13870.2520.2322-0.0078-0.00540.048805.08520.09150.18053.0719-0.23572.7757-58.49933.934-3.719
420.1596-0.5957-0.18270.02420.0846-0.46360.2855-0.34520.5683-0.8919-0.0152-0.3206-0.47030.238802.9887-0.0871-0.28482.5517-0.05252.6289-82.67991.99-75.562
43-0.2350.02460.0428-0.05630.10740.11950.108-0.66130.28930.6255-0.19041.5140.0877-0.0918-03.270.05370.04812.99980.12634.1286-106.25677.368-61.93
440.65591.34630.55731.29310.86152.2641-0.6360.24280.8298-0.48220.161-0.1939-0.63180.368202.3004-0.2063-0.14812.07850.15952.1911-53.06874.395-70.682
45-0.05240.54790.23710.34380.25130.6895-0.1985-0.37640.12380.53440.2020.1656-0.7543-0.079702.9474-0.2293-0.14452.3010.02682.3157-43.44673.895-10.574
460.3582-0.0792-0.21530.0892-0.0181-0.0138-0.05430.88310.0404-0.14370.0932-0.3051-0.78431.4154-02.7454-0.4322-0.25833.1340.07732.6628-55.3536.69360.464
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 49
2X-RAY DIFFRACTION2A50 - 179
3X-RAY DIFFRACTION3A180 - 233
4X-RAY DIFFRACTION4A234 - 235
5X-RAY DIFFRACTION5B6 - 49
6X-RAY DIFFRACTION6B50 - 179
7X-RAY DIFFRACTION7B180 - 233
8X-RAY DIFFRACTION8C3 - 158
9X-RAY DIFFRACTION9C159 - 370
10X-RAY DIFFRACTION10C371 - 481
11X-RAY DIFFRACTION11C482 - 703
12X-RAY DIFFRACTION12C704 - 883
13X-RAY DIFFRACTION13C884 - 1037
14X-RAY DIFFRACTION14C1038 - 1252
15X-RAY DIFFRACTION15C1253 - 1342
16X-RAY DIFFRACTION16D8 - 332
17X-RAY DIFFRACTION17D333 - 1376
18X-RAY DIFFRACTION18E2 - 60
19X-RAY DIFFRACTION19E61 - 90
20X-RAY DIFFRACTION20F94 - 262
21X-RAY DIFFRACTION21F263 - 354
22X-RAY DIFFRACTION22F355 - 530
23X-RAY DIFFRACTION23F531 - 612
24X-RAY DIFFRACTION24G7 - 49
25X-RAY DIFFRACTION25G50 - 179
26X-RAY DIFFRACTION26G180 - 233
27X-RAY DIFFRACTION27H6 - 49
28X-RAY DIFFRACTION28H50 - 179
29X-RAY DIFFRACTION29H180 - 233
30X-RAY DIFFRACTION30I3 - 158
31X-RAY DIFFRACTION31I159 - 370
32X-RAY DIFFRACTION32I371 - 481
33X-RAY DIFFRACTION33I482 - 703
34X-RAY DIFFRACTION34I704 - 883
35X-RAY DIFFRACTION35I884 - 1037
36X-RAY DIFFRACTION36I1038 - 1252
37X-RAY DIFFRACTION37I1253 - 1342
38X-RAY DIFFRACTION38J16 - 332
39X-RAY DIFFRACTION39J333 - 1375
40X-RAY DIFFRACTION40K2 - 60
41X-RAY DIFFRACTION41K61 - 80
42X-RAY DIFFRACTION42L94 - 262
43X-RAY DIFFRACTION43L263 - 354
44X-RAY DIFFRACTION44L355 - 530
45X-RAY DIFFRACTION45L531 - 613
46X-RAY DIFFRACTION46B246 - 317

+
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