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- PDB-5w4u: Pol II elongation complex with an N6-methyladenine-containing template -

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Basic information

Entry
Database: PDB / ID: 5w4u
TitlePol II elongation complex with an N6-methyladenine-containing template
Components
  • (DNA-directed RNA polymerase II subunit ...) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • 14mer non-template DNA
  • 29mer template DNA
  • 9mer RNA
KeywordsDNA BINDING PROTEIN/RNA/DNA / Complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-RNA-DNA complex
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / peroxisome / ribosome biogenesis / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 ...Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / N-terminal domain of TfIIb - #10 / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Gyrase A; domain 2 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / Homeodomain-like / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Single Sheet / Nucleic acid-binding proteins / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / 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 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / DNA-directed RNA polymerase, insert domain
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 ...DNA / DNA (> 10) / RNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsWang, W. / Wang, D.
CitationJournal: J.Am.Chem.Soc. / Year: 2017
Title: Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing.
Authors: Wang, W. / Xu, L. / Hu, L. / Chong, J. / He, C. / Wang, D.
History
DepositionJun 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase II subunit RPB2
C: DNA-directed RNA polymerase II subunit RPB3
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
T: 29mer template DNA
N: 14mer non-template DNA
R: 9mer RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)486,30122
Polymers485,75313
Non-polymers5489
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area65220 Å2
ΔGint-394 kcal/mol
Surface area141090 Å2
Unit cell
Length a, b, c (Å)167.210, 221.990, 192.700
Angle α, β, γ (deg.)90.00, 100.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

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DNA-directed RNA polymerase II subunit ... , 5 types, 5 molecules ABCIK

#1: Protein DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P16370
#7: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P27999
#9: Protein DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38902

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#4: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20434
#5: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20435
#6: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20436
#8: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P22139
#10: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40422

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DNA chain , 2 types, 2 molecules TN

#11: DNA chain 29mer template DNA


Mass: 8865.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#12: DNA chain 14mer non-template DNA


Mass: 4286.789 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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RNA chain , 1 types, 1 molecules R

#13: RNA chain 9mer RNA


Mass: 2974.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Non-polymers , 2 types, 9 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 66.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 50mM dioxane, 10mM DTT, 10-12.5% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→95.8 Å / Num. obs: 79907 / % possible obs: 100 % / Redundancy: 5.4 % / Net I/σ(I): 5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NVZ

2nvz


Resolution: 3.6→81.021 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 3545 4.97 %
Rwork0.227 --
obs0.2286 71390 89.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→81.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27742 1070 9 0 28821
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00229449
X-RAY DIFFRACTIONf_angle_d0.51439990
X-RAY DIFFRACTIONf_dihedral_angle_d12.21411253
X-RAY DIFFRACTIONf_chiral_restr0.0214495
X-RAY DIFFRACTIONf_plane_restr0.0024989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6004-3.64980.3391470.3161648X-RAY DIFFRACTION21
3.6498-3.70190.3407540.31481236X-RAY DIFFRACTION41
3.7019-3.75720.3378870.29081679X-RAY DIFFRACTION54
3.7572-3.81590.3091810.2961940X-RAY DIFFRACTION65
3.8159-3.87840.31291080.30682280X-RAY DIFFRACTION75
3.8784-3.94530.38321530.30162552X-RAY DIFFRACTION85
3.9453-4.0170.3171580.28282821X-RAY DIFFRACTION94
4.017-4.09430.29231500.27433084X-RAY DIFFRACTION100
4.0943-4.17790.29031750.2672978X-RAY DIFFRACTION100
4.1779-4.26870.29731820.25333010X-RAY DIFFRACTION100
4.2687-4.3680.25761490.23483015X-RAY DIFFRACTION100
4.368-4.47720.25391280.22463076X-RAY DIFFRACTION100
4.4772-4.59830.2331460.21663025X-RAY DIFFRACTION100
4.5983-4.73360.23241540.20283033X-RAY DIFFRACTION100
4.7336-4.88630.24731750.20843024X-RAY DIFFRACTION100
4.8863-5.0610.23181630.21573019X-RAY DIFFRACTION100
5.061-5.26360.25991620.21833010X-RAY DIFFRACTION100
5.2636-5.50310.27921450.22333071X-RAY DIFFRACTION100
5.5031-5.79310.2841500.22843067X-RAY DIFFRACTION100
5.7931-6.1560.25351530.22393015X-RAY DIFFRACTION100
6.156-6.63110.2281690.22993052X-RAY DIFFRACTION100
6.6311-7.2980.2441490.2173062X-RAY DIFFRACTION100
7.298-8.35310.18771570.17573045X-RAY DIFFRACTION100
8.3531-10.52040.19921780.15023042X-RAY DIFFRACTION100
10.5204-81.04120.22491720.19273061X-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)
11.34090.4664-0.15131.82760.32041.870.0950.14660.48060.1670.0472-0.8462-0.39361.2726-0.07790.5096-0.1507-0.03871.5468-0.01521.842482.8626-15.1367418.3323
22.31640.6317-0.01361.5208-0.22421.60990.28070.25960.05930.0708-0.0407-0.14140.39530.1536-0.13760.31050.0453-0.06990.1339-0.00840.247439.1414-41.0048411.7024
30.212-0.0968-0.17751.76430.38010.80170.2346-0.3349-0.1820.87220.0134-0.19330.5424-0.2852-0.0450.6347-0.1665-0.02340.35180.18430.347425.7122-34.1069444.6311
40.38080.01010.23371.2033-0.37070.50780.0935-0.1277-0.14080.58360.15660.05590.47150.0211-0.06181.10110.1624-0.36540.21280.04120.6576450.253-57.2259448.7079
51.84140.5991.49855.93584.16634.36220.0692-0.4882-0.09810.96590.0628-0.23830.40040.0058-0.11951.80620.0834-0.27040.574-0.03810.833458.9598-13.3278487.4616
60.4320.0903-0.4291.11311.26892.1878-0.0558-0.28180.1040.97830.0891-0.3313-0.2593-0.013-0.17941.2240.2273-0.40690.4644-0.070.6435453.0298-39.7776458.272
70.98050.2529-0.27840.6119-1.18482.75620.05180.2130.38730.72870.348-1.03130.04960.8201-0.0570.4760.1298-0.26280.6504-0.02530.942468.4351-36.7139424.3464
82.17150.71530.13372.3032-0.79261.54770.2673-0.28550.46060.2384-0.1717-0.2024-0.69610.0515-0.16290.7667-0.17690.37460.15890.06730.3985427.04314.2795431.2409
91.15531.28360.22312.4715-0.12740.1923-0.00820.25660.4874-0.44290.0650.0679-0.49540.1449-0.07690.6907-0.17280.21740.37970.19050.4502430.906815.3988411.8725
101.47480.62421.8060.8591.83844.26480.235-0.19530.07790.45260.2288-0.36980.21970.4321-0.36171.0374-0.1751-0.11540.3404-0.06140.6811452.71266.2615451.8872
114.33570.08230.87953.5485-0.44346.8327-0.21570.5060.43560.4371-0.1167-0.6911-0.92621.04980.3360.9964-0.19080.00850.5571-0.07070.752461.859716.7305456.7429
120.57870.18190.77890.93660.17561.00850.32760.10860.24240.05050.2699-0.2686-0.15580.2428-0.29780.5995-0.17960.15230.45440.08910.7832448.059610.6563433.6014
130.8260.3333-0.4821.09640.07091.82850.0841-0.19890.01570.1916-0.0165-0.2024-0.19680.24120.12850.309-0.03970.26420.14760.11650.2464432.3235-0.8315434.2175
146.66050.80132.47743.21222.05613.84280.0348-0.73490.40910.54060.1748-0.1729-0.1147-0.0937-0.15530.8132-0.02450.16650.2652-0.02010.3935433.169417.2989455.6366
156.6110.75010.93144.32240.8071.92150.1691-0.23520.5070.082-0.0730.6439-0.9086-0.6543-0.10230.4910.12910.19090.40410.15270.378412.85349.5655443.8977
160.71630.08880.53471.6268-0.0290.96490.0197-0.07020.19830.72920.06450.0837-0.0036-0.4240.01830.3385-0.00910.36610.31890.14110.1042417.9754-8.9687436.6544
170.5535-0.04420.43771.23180.02141.18440.13480.2661-0.0067-0.45250.0658-0.1822-0.30620.3260.02550.3423-0.24650.28950.49940.15770.0884426.3051-14.4533406.8364
181.66310.9889-1.12032.5253-1.00572.6511-0.09950.23640.0329-0.29840.0712-0.19090.03520.13240.01110.2325-0.03650.01230.37830.10480.2298427.058-17.2997405.0901
190.2609-0.03810.61891.1913-0.06181.28260.12070.26590.19320.0762-0.0598-0.45750.170.3242-0.08330.1692-0.11150.05020.29380.14940.4188442.9426-28.7934415.4331
202.12290.4806-0.75151.7088-0.49061.3827-0.2248-0.2323-0.1958-0.23430.00690.5620.0878-0.5194-0.18520.2832-0.3014-0.19170.93840.20010.3472395.3801-38.4604404.8713
211.27690.3786-0.41312.90290.43121.4286-0.0210.61080.0235-0.23-0.07610.3326-0.1187-0.47350.08490.24630.0431-0.02580.76120.13610.298403.9252-18.5088392.66
221.89050.8492-0.64573.7434-0.76811.9690.0214-0.2895-0.18930.5981-0.15720.52510.0573-0.2799-0.04630.4193-0.41690.03980.71320.19130.4725396.0607-41.1208429.6132
232.9172-2.02271.72194.8924-1.42234.0206-0.0772-0.2753-0.74210.6997-0.01490.1370.0247-0.44820.07490.7396-0.5023-0.15081.27860.24311.0438389.7-51.9929426.9864
241.9119-1.21350.68333.8831-1.75960.92550.29490.5716-0.0982-0.9004-0.23730.51730.2815-0.1186-0.03240.4325-0.2913-0.20960.7042-0.05540.502399.4254-44.7862398.3283
251.52070.2360.14210.08610.39762.8728-0.4331-0.8260.33020.7310.2459-0.1725-0.19490.3794-0.12181.84740.4033-1.0141.1874-0.2721.2353474.9314-49.4736475.4678
260.3487-0.48350.1061.0205-0.35380.15280.1483-0.58450.4881.00440.8116-1.39570.39480.6329-0.82441.47410.2672-0.84811.4951-0.39661.9016484.5502-44.9416468.3482
270.3504-0.4657-0.99130.67621.38662.88810.0888-0.6508-0.04180.56790.531-1.33040.12970.7548-0.65411.534-0.0544-0.83562.0888-0.56072.7217493.2162-39.4479469.4624
281.2862-1.3963-0.6941.62130.35481.8091-0.054-0.07090.98351.01740.5882-1.450.09940.9628-0.07041.14460.3005-0.71770.9681-0.16831.5494478.8803-44.8491458.5649
290.9558-0.99440.26631.1478-0.54970.695-0.08310.03690.49610.3226-0.0892-0.7981-0.0460.38160.39691.00860.3446-0.65710.4729-0.05911.0612471.6364-48.8204446.5715
305.7571-2.03991.22992.5866-1.64313.6760.08050.0707-0.23510.67970.1506-1.11360.54690.7551-0.07470.90130.2253-0.26120.4442-0.02470.6986461.7006-59.472415.5602
313.8007-0.85721.49162.0868-0.53180.61770.31420.4106-0.8545-0.6075-0.1553-0.45930.68610.3918-0.12951.07210.244-0.06270.7274-0.06750.8085450.5956-61.9153398.2078
321.7792-1.60231.40618.2167-8.09697.9999-0.0592-0.0907-1.29990.50050.30671.36710.5386-0.1397-0.23510.98270.3204-0.21920.4198-0.0620.8712449.564-61.3573406.0789
333.0518-1.95690.6074.50482.22482.2407-0.1537-0.2469-0.2177-0.30860.72-0.24740.5060.2351-0.49930.9420.0651-0.02640.4743-0.0070.4872462.7757-61.7252411.9736
346.6906-5.0118-7.76715.18966.99589.98321.1064-1.6456-0.24780.5399-0.6541-2.0892-0.02981.023-0.4050.5067-0.19930.02950.81740.26911.4405473.6782-53.6918425.1526
353.5746-1.9773-1.76037.7884-0.9599.46510.3664-0.0235-0.00820.01690.1746-0.2897-0.25790.2987-0.45191.45780.5026-0.21020.7548-0.21611.0407468.8419-61.9447418.3065
369.00944.9645-1.06796.5648-4.44784.95950.58650.8605-0.1799-0.1086-0.3461.2299-0.4699-0.5611-0.29211.05480.3931-0.30530.5348-0.13670.8999456.8794-65.8527417.1049
373.0881-0.635-1.71683.2846-1.91632.59240.2497-0.7116-0.09180.7801-0.44310.64060.4755-0.05410.12251.0253-0.53420.18021.04730.19930.9395405.1453-67.484444.0755
382.24810.8909-1.24275.6892-1.32951.74730.1841-0.7098-0.3850.7947-0.24320.16650.15460.1260.03341.2318-0.5068-0.03540.67480.41081.1527402.795-70.7426443.9106
395.90226.2857-5.44978.1967-6.3635.2394-0.21050.077-0.4749-0.7525-0.13610.18040.06590.03630.28851.9278-0.3628-0.29530.61410.18091.3664409.683-74.3948420.3114
404.38394.074-5.45958.6515-6.20867.4574-0.23560.89940.7338-1.33120.80720.3368-0.6291-0.3242-0.56051.9447-0.7246-0.01620.9908-0.02322.0285399.4971-77.2521421.742
411.66761.148-1.12614.273-1.35922.1030.0325-0.1994-0.2956-0.0293-0.11570.00220.09250.15610.00661.4118-0.2426-0.30340.59090.4491.0808412.6908-72.573437.4437
425.1957-1.81961.44568.631.17494.4562-0.497-0.8097-1.00970.92550.08650.36980.96350.03510.29071.3694-0.24-0.12320.70980.5071.291417.2359-75.9599446.3547
432.7335-2.66030.06469.4543-2.57063.34810.0208-0.0992-1.008-0.59170.582-0.11731.4495-0.1241-0.47631.5926-0.4428-0.2420.86250.2910.8946415.1328-76.2921440.1852
447.2936.6066-2.2817.548-3.25555.48620.4222-0.23950.75391.2092-0.02981.25230.5012-0.7715-0.56211.3208-0.29840.16970.48790.28051.4179401.3549-74.6484435.5768
450.48520.3505-0.50945.15550.02650.655-0.0084-0.1307-0.01410.26920.1847-0.23070.18110.1895-0.17221.46-0.1345-0.20580.5808-0.33470.7037459.947810.2393482.5165
465.4592-0.9285-3.14933.8373.03444.82980.6113-0.26320.2511-0.4008-0.31510.0851-0.27590.3047-0.25920.8180.01780.09640.5489-0.03970.3266423.57751.3983471.6534
473.2614-4.8394-2.80038.25375.02858.87530.1437-0.2670.24740.18630.4216-0.63720.63430.7148-0.43710.4396-0.12580.16740.6848-0.06270.398431.3361-5.2202473.2523
481.005-0.1629-1.51230.2841-0.0287.31250.0919-0.24060.01290.0521-0.1683-0.0602-0.1280.7805-0.04560.36870.02310.33080.32330.08290.2681407.1921-12.7476407.1217
491.1628-1.4852.86081.9752-3.82027.3912-0.21980.37180.1268-0.03160.02660.2130.0117-0.36770.13210.1862-0.02790.04550.61110.04080.4613404.827-24.096409.6632
504.19841.0328-1.6232.1892-0.73.27030.22610.46980.1971-0.0103-0.27410.2308-0.1646-0.55980.10390.20030.08630.2670.4229-0.06480.4686398.2573-18.7311407.4062
515.30610.76421.34832.0603-1.92683.72550.1046-0.03040.57850.37620.04650.9248-0.5556-0.7467-0.22430.25870.21290.2120.7482-0.11020.677395.3195-7.3269412.8517
529.49643.67142.49289.51976.62484.6106-0.16080.41360.5174-0.1883-0.4732-0.4944-0.80930.89120.61360.54650.1920.07961.1970.29261.3762389.4303-5.5259419.0823
530.7447-0.0301-0.85692.78611.61233.0658-0.1077-0.04170.09630.0079-0.00910.2559-0.0401-0.2893-0.08070.1254-0.0140.11770.7541-0.01260.734393.4445-17.5879417.1459
541.9962-0.38180.79560.9986-0.36340.39260.1342-0.2005-0.13610.0857-0.05440.09370.04470.04330.06560.3324-0.05430.15810.48250.110.2027401.8239-19.8389417.1613
551.96532.1881-0.84852.7046-0.67810.63390.16960.69770.67480.16010.20840.4619-0.2125-0.1661-0.37150.3247-0.26620.30520.4760.03030.4048407.5315-9.2851413.6073
569.02120.50641.98112.3073-0.48252.0628-0.02120.33370.6353-0.61170.32920.2255-0.7117-0.3646-0.27550.3520.03460.05660.43780.18760.685411.82181.4591405.8487
573.6442-1.4608-0.08284.680.64085.3638-0.37290.5334-0.1536-0.3366-0.2653-0.1692-0.3931-0.86020.62910.4273-0.0383-0.02540.5244-0.01450.3479421.2451-34.4891398.7929
584.95010.73311.05345.02381.12553.12460.58490.3362-0.67740.0193-0.4114-1.11530.54020.2094-0.06940.3421-0.21030.0790.7195-0.04550.7328418.2311-56.079397.8974
596.14282.06250.98952.9862-3.29176.00520.3260.0928-0.28950.6620.3841-0.44310.4465-0.1842-0.59340.5546-0.0402-0.11650.4943-0.05840.2344414.7352-53.1731400.8798
600.2650.3846-0.17824.86770.85560.4075-0.02490.0442-0.49590.3096-0.2770.66470.2612-0.34490.24810.5256-0.3101-0.09360.39970.04750.5837405.6065-52.9085407.2467
611.16160.312-1.14814.18511.96362.38980.05320.2147-0.61910.1531-0.19870.8980.6205-0.82210.2290.7377-0.2694-0.39770.57610.04130.953406.7307-62.491409.8102
625.97654.81854.38865.15335.31525.7120.08480.3692-0.61550.02540.2334-0.33460.6030.2611-0.36690.578-0.0887-0.2560.2533-0.0580.3445420.8252-44.5787406.9489
631.8163-0.58770.88432.43950.88572.51820.36870.1182-0.82180.010.14970.0050.7493-0.1391-0.19610.6307-0.0689-0.35560.3495-0.16920.4726414.5086-58.4279405.6235
644.3777-0.6699-2.71484.02023.90274.78830.27070.6602-0.99520.0429-0.09290.24970.8082-0.0731-0.16961.2397-0.2292-0.30980.8665-0.18381.444407.8509-72.5013402.6983
652.431-0.33730.50050.5855-0.15041.6050.56070.6764-1.0175-0.0474-0.46731.00460.4771-0.6565-0.00990.402-0.2345-0.05650.8653-0.02980.8598391.744-49.8053400.8486
662.96740.91931.93778.5833-6.14397.53960.7060.850.1591-0.3291-0.1380.0476-1.0999-0.3721-0.52661.2139-0.0628-0.29571.31440.56371.0768425.91973.4231387.4775
675.7345-2.874-4.70134.4391-1.19579.10040.1470.4311.1011-1.0239-0.4391.4614-1.6476-2.42360.27881.71120.0994-0.19081.52590.30561.3427420.4519.3367394.5013
687.46115.71486.81074.37815.21556.21840.13620.94550.6128-0.7555-0.0046-0.3037-0.63640.1573-0.13741.7329-0.23640.03461.43920.72451.2688426.41547.4172383.9132
699.44450.1958-4.61087.8447-2.32662.89180.71820.53530.6478-0.96680.022-0.8508-1.3371-0.0605-0.76912.3295-0.37220.19911.8108-0.06962.237436.06668.8844385.1766
703.38553.259-1.80727.53040.9662.6360.35250.37471.1052-0.23790.00450.0533-1.2283-0.454-0.36282.0598-0.02760.2461.38780.50051.7957425.62215.5998390.8003
715.2712.0412-0.66494.3869-4.14435.81380.2893-0.86320.41530.6643-0.6269-0.0706-1.8310.56870.28541.0175-0.21620.02110.89570.2320.3612428.20598.1854394.8289
721.46762.8585-0.8776.4155-2.00070.6242-0.4120.45010.0334-1.6830.0261-0.19980.21440.12150.31770.88160.0636-0.0461.16990.13020.2913418.8425-14.7781388.8723
732.146-0.4158-1.15993.6022-0.10980.6659-0.1988-1.38040.48671.63420.0253-1.0815-0.27110.64590.1683.6425-0.0668-0.71343.3621-0.3233.0259490.8869-12.8229466.4897
742.6944-0.1062-2.16568.3335-1.77863.9442-0.05910.53910.1294-0.0797-0.15350.42450.12720.19460.13383.23760.0348-0.30093.1735-0.21712.9426470.477-13.7923452.44
754.69051.3982-0.1733.5581.21050.5146-0.5985-0.5021.03750.78570.039-1.6628-1.32991.15980.52971.1-0.1174-0.3850.8792-0.1041.0071449.2591-14.287420.2533
760.1498-0.8010.56514.5957-1.708770.05850.42480.7628-0.3615-0.3762-0.1182-0.59850.36890.33332.33250.57710.00732.877-0.11582.7864479.9071-15.945457.0712
771.1345-1.40.76652.31880.87776.1395-0.2507-0.3301-0.1943-0.653-0.1036-0.789-0.23841.6110.31120.5090.03640.10010.6171-0.02440.6689444.1613-13.0768418.4428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 304 )
2X-RAY DIFFRACTION2chain 'A' and (resid 305 through 578 )
3X-RAY DIFFRACTION3chain 'A' and (resid 579 through 844 )
4X-RAY DIFFRACTION4chain 'A' and (resid 845 through 1166 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1167 through 1268 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1269 through 1376 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1377 through 1449 )
8X-RAY DIFFRACTION8chain 'B' and (resid 20 through 94 )
9X-RAY DIFFRACTION9chain 'B' and (resid 95 through 202 )
10X-RAY DIFFRACTION10chain 'B' and (resid 203 through 307 )
11X-RAY DIFFRACTION11chain 'B' and (resid 308 through 371 )
12X-RAY DIFFRACTION12chain 'B' and (resid 372 through 479 )
13X-RAY DIFFRACTION13chain 'B' and (resid 480 through 559 )
14X-RAY DIFFRACTION14chain 'B' and (resid 560 through 633 )
15X-RAY DIFFRACTION15chain 'B' and (resid 634 through 700 )
16X-RAY DIFFRACTION16chain 'B' and (resid 701 through 791 )
17X-RAY DIFFRACTION17chain 'B' and (resid 792 through 892 )
18X-RAY DIFFRACTION18chain 'B' and (resid 893 through 1022 )
19X-RAY DIFFRACTION19chain 'B' and (resid 1023 through 1220 )
20X-RAY DIFFRACTION20chain 'C' and (resid 3 through 51 )
21X-RAY DIFFRACTION21chain 'C' and (resid 52 through 176 )
22X-RAY DIFFRACTION22chain 'C' and (resid 177 through 207 )
23X-RAY DIFFRACTION23chain 'C' and (resid 208 through 227 )
24X-RAY DIFFRACTION24chain 'C' and (resid 228 through 268 )
25X-RAY DIFFRACTION25chain 'E' and (resid 3 through 71 )
26X-RAY DIFFRACTION26chain 'E' and (resid 72 through 89 )
27X-RAY DIFFRACTION27chain 'E' and (resid 90 through 103 )
28X-RAY DIFFRACTION28chain 'E' and (resid 104 through 167 )
29X-RAY DIFFRACTION29chain 'E' and (resid 168 through 215 )
30X-RAY DIFFRACTION30chain 'F' and (resid 72 through 102 )
31X-RAY DIFFRACTION31chain 'F' and (resid 103 through 116 )
32X-RAY DIFFRACTION32chain 'F' and (resid 117 through 126 )
33X-RAY DIFFRACTION33chain 'F' and (resid 127 through 137 )
34X-RAY DIFFRACTION34chain 'F' and (resid 138 through 142 )
35X-RAY DIFFRACTION35chain 'F' and (resid 143 through 147 )
36X-RAY DIFFRACTION36chain 'F' and (resid 148 through 155 )
37X-RAY DIFFRACTION37chain 'H' and (resid 3 through 30 )
38X-RAY DIFFRACTION38chain 'H' and (resid 31 through 60 )
39X-RAY DIFFRACTION39chain 'H' and (resid 61 through 82 )
40X-RAY DIFFRACTION40chain 'H' and (resid 83 through 92 )
41X-RAY DIFFRACTION41chain 'H' and (resid 93 through 106 )
42X-RAY DIFFRACTION42chain 'H' and (resid 107 through 118 )
43X-RAY DIFFRACTION43chain 'H' and (resid 119 through 140 )
44X-RAY DIFFRACTION44chain 'H' and (resid 141 through 146 )
45X-RAY DIFFRACTION45chain 'I' and (resid 2 through 52 )
46X-RAY DIFFRACTION46chain 'I' and (resid 53 through 86 )
47X-RAY DIFFRACTION47chain 'I' and (resid 87 through 116 )
48X-RAY DIFFRACTION48chain 'J' and (resid 1 through 5 )
49X-RAY DIFFRACTION49chain 'J' and (resid 6 through 10 )
50X-RAY DIFFRACTION50chain 'J' and (resid 11 through 17 )
51X-RAY DIFFRACTION51chain 'J' and (resid 18 through 26 )
52X-RAY DIFFRACTION52chain 'J' and (resid 27 through 31 )
53X-RAY DIFFRACTION53chain 'J' and (resid 32 through 43 )
54X-RAY DIFFRACTION54chain 'J' and (resid 44 through 51 )
55X-RAY DIFFRACTION55chain 'J' and (resid 52 through 56 )
56X-RAY DIFFRACTION56chain 'J' and (resid 57 through 65 )
57X-RAY DIFFRACTION57chain 'K' and (resid 1 through 9 )
58X-RAY DIFFRACTION58chain 'K' and (resid 10 through 29 )
59X-RAY DIFFRACTION59chain 'K' and (resid 30 through 39 )
60X-RAY DIFFRACTION60chain 'K' and (resid 40 through 50 )
61X-RAY DIFFRACTION61chain 'K' and (resid 51 through 62 )
62X-RAY DIFFRACTION62chain 'K' and (resid 63 through 69 )
63X-RAY DIFFRACTION63chain 'K' and (resid 70 through 77 )
64X-RAY DIFFRACTION64chain 'K' and (resid 78 through 82 )
65X-RAY DIFFRACTION65chain 'K' and (resid 83 through 114 )
66X-RAY DIFFRACTION66chain 'L' and (resid 27 through 31 )
67X-RAY DIFFRACTION67chain 'L' and (resid 32 through 36 )
68X-RAY DIFFRACTION68chain 'L' and (resid 37 through 41 )
69X-RAY DIFFRACTION69chain 'L' and (resid 42 through 46 )
70X-RAY DIFFRACTION70chain 'L' and (resid 47 through 51 )
71X-RAY DIFFRACTION71chain 'L' and (resid 52 through 58 )
72X-RAY DIFFRACTION72chain 'L' and (resid 59 through 70 )
73X-RAY DIFFRACTION73chain 'T' and (resid 1 through 6 )
74X-RAY DIFFRACTION74chain 'T' and (resid 8 through 14 )
75X-RAY DIFFRACTION75chain 'T' and (resid 15 through 29 )
76X-RAY DIFFRACTION76chain 'N' and (resid 1 through 14 )
77X-RAY DIFFRACTION77chain 'R' and (resid 1 through 9 )

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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

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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

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