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- PDB-5g5l: RNA polymerase I-Rrn3 complex at 4.8 A resolution -

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Entry
Database: PDB / ID: 5g5l
TitleRNA polymerase I-Rrn3 complex at 4.8 A resolution
Components
  • (DNA-DIRECTED RNA POLYMERASE I SUBUNIT ...Polymerase) x 7
  • (DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT ...) x 2
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ...RNA polymerase) x 5
  • RNA POLYMERASE I-SPECIFIC TRANSCRIPTION INITIATION FACTOR RRN3
KeywordsRNA POLYMERASE / TRANSCIPTION
Function / homologyRPA43 OB domain in RNA Pol I / RNA polymerases N / 8 kDa subunit / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb3/RpoA insert domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb6 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 ...RPA43 OB domain in RNA Pol I / RNA polymerases N / 8 kDa subunit / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb3/RpoA insert domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb6 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb8 / RNA polymerase Rpb5, N-terminal domain / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 6 / DNA-directed RNA polymerase subunit Rpb5-like / RNA polymerase Rpb2, domain 3 / Pol I subunit A12, C-terminal zinc ribbon / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerases I and III subunit AC40 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb1, funnel domain superfamily / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase, subunit H/Rpb5, conserved site / mRNA Splicing - Minor Pathway / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / TP53 Regulates Transcription of DNA Repair Genes / RNA polymerase II transcribes snRNA genes / mRNA Capping / RNA Polymerase I Transcription Initiation / Formation of the Early Elongation Complex / 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 / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA Polymerase II Pre-transcription Events / Zinc finger TFIIS-type profile. / RNA polymerase Rpb1, domain 1 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase I specific transcription initiation factor RRN3 / A49-like RNA polymerase I associated factor / RNA polymerase I, Rpa2 specific domain / Yeast RNA polymerase I subunit RPA14 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases beta chain signature. / RNA polymerases D / 30 to 40 Kd subunits signature. / Zinc finger TFIIS-type signature. / RNA polymerases M / 15 Kd subunits signature. / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase Rpb7, N-terminal / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 3 / RNA polymerase, N-terminal / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase, Rpb5, N-terminal / RNA polymerase, beta subunit, conserved site / RNA polymerase, Rpb8 / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / Zinc finger, TFIIS-type / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit N/Rpb10 / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase, subunit omega/K/RPB6 / RNA polymerase Rpb2, domain 7 / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA pol I, largest subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, OB-fold
Function and homology information
Specimen sourceSACCHAROMYCES CEREVISIAE (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.8 Å resolution
AuthorsEngel, C. / Plitzko, J. / Cramer, P.
CitationJournal: Nat Commun / Year: 2016
Title: RNA polymerase I-Rrn3 complex at 4.8 Å resolution.
Authors: Christoph Engel / Jürgen Plitzko / Patrick Cramer
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 26, 2016 / Release: Jul 27, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 27, 2016Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collectionem_software_em_software.fitting_id / _em_software.image_processing_id / _em_software.name
1.2Jun 20, 2018Structure modelAdvisory / Data collection / Derived calculationspdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type_pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn_type.id
1.3Oct 24, 2018Structure modelAdvisory / Data collection / Derived calculationspdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BN" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -4-STRANDED BARREL THIS IS REPRESENTED BY A -3-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "MB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -3-STRANDED BARREL THIS IS REPRESENTED BY A -2-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190
B: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135
C: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1
D: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14
E: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
G: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
I: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
K: DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
M: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49
N: DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34
O: RNA POLYMERASE I-SPECIFIC TRANSCRIPTION INITIATION FACTOR RRN3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)663,19522
Polyers662,73715
Non-polymers4587
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA-DIRECTED RNA POLYMERASE I SUBUNIT ... , 7 types, 7 molecules ABDGIMN

#1: Protein/peptide DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190 / Polymerase / DNA-DIRECTED RNA POLYMERASE I 190 KDA POLYPEPTIDE / A190 / DNA-DIRECTED RNA POLYMERASE I LARGEST SUBUNIT


Mass: 186676.969 Da / Num. of mol.: 1 / Details: C-TERMINAL FLAG-10XHIS TAG / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P10964, DNA-directed RNA polymerase
#2: Protein/peptide DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135 / Polymerase / DNA-DIRECTED RNA POLYMERASE I 135 KDA POLYPEPTIDE / A135 / DNA-DIRECTED RNA POLYMERASE I POLYPEPTIDE 2 / RNA POLYMERASE I SUBUNIT 2


Mass: 135910.328 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P22138, DNA-directed RNA polymerase
#4: Protein/peptide DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14 / Polymerase / A14 / DNA-DIRECTED RNA POLYMERASE I 14 KDA POLYPEPTIDE


Mass: 14599.128 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P50106
#7: Protein/peptide DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43 / Polymerase / A43 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 36 KDA POLYPEPTIDE


Mass: 36264.852 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P46669
#9: Protein/peptide DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12 / Polymerase / A12 / A12.2 / DNA-DIRECTED RNA POLYMERASE I 13.7 KDA POLYPEPTIDE


Mass: 13676.566 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P32529
#13: Protein/peptide DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49 / Polymerase / A49 / DNA-DIRECTED RNA POLYMERASE I 49 KDA POLYPEPTIDE


Mass: 46721.707 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: Q01080
#14: Protein/peptide DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34 / Polymerase / A34 / DNA-DIRECTED DNA-DEPENDENT RNA POLYMERASE 34.5 KDA POLYPEPTIDE / A34.5


Mass: 26933.518 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P47006

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DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT ... , 2 types, 2 molecules CK

#3: Protein/peptide DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1 / RNA POLYMERASES I AND III SUBUNIT AC1 / C37 / DNA-DIRECTED RNA POLYMERASES I AND III 40 KDA POLYPEPTIDE / AC40 / C40


Mass: 37732.613 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P07703
#11: Protein/peptide DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2 / RNA POLYMERASES I AND III SUBUNIT AC2 / AC19 / DNA-DIRECTED RNA POLYMERASES I AND III 16 KDA POLYPEPTIDE / RPA19


Mass: 16167.860 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P28000

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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC ... , 5 types, 5 molecules EFHJL

#5: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 1


Mass: 25117.094 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P20434
#6: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / DNA-DIR DNA-DIRECTED RNA POLYMERASES I / II / AND III 23 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 2


Mass: 17931.834 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P20435
#8: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 14.5 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 3


Mass: 16525.363 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P20436
#10: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 8.3 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 5


Mass: 8290.732 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P22139
#12: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA / DNA-DIRECTED RNA POLYMERASES I / II / AND III SUBUNIT RPABC 4


Mass: 7729.969 Da / Num. of mol.: 1 / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / Strain: CB010 / References: UniProt: P40422

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Protein/peptide / Non-polymers , 2 types, 8 molecules O

#15: Protein/peptide RNA POLYMERASE I-SPECIFIC TRANSCRIPTION INITIATION FACTOR RRN3 / RNA POLYMERASE I-SPECIFIC TRANSCRIPTION INITIATION FACTOR RRN3


Mass: 72458.258 Da / Num. of mol.: 1
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Strain: CB010 / Plasmid name: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P36070
#16: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Formula: Zn / Zinc

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Details

Sequence detailsC-TERMINAL FLAG-10XHIS TAG

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: S. CEREVISIAE RNA POLYMERASE I BOUND TO THE INITIATION FACTOR RRN3
Type: COMPLEX
Buffer solutionName: 150MM NACL, 5MM HEPES, 1MM MGCL2, 0.01 MM ZNCL2, 5 MM DTT
Details: 150MM NACL, 5MM HEPES, 1MM MGCL2, 0.01 MM ZNCL2, 5 MM DTT
pH: 7.8
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITROBOT MARK IV, METHOD- 4.5 MICROLITERS OF SAMPLE WAS APPLIED TO GLOW- DISCHARGED QUANTIFOIL R 2- 1 HOLEY CARBON GRIDS, WHICH WERE THEN BLOTTED FOR 8.5S AND PLUNGE- FROZEN IN LIQUID ETHANE.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Mar 27, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 37000 / Calibrated magnification: 37037 / Nominal defocus max: 3600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNumber digital images: 1174

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2UCSF Chimeramodel fitting
3RELION3D reconstruction
CTF correctionDetails: RELION
SymmetryPoint symmetry: C1
3D reconstructionMethod: RELIONList of Walmart brands / Resolution: 4.8 Å / Number of particles: 63445 / Nominal pixel size: 1.35 / Actual pixel size: 1.35
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3439. (DEPOSITION ID: 14566).
Symmetry type: POINT
Atomic model buildingDetails: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY / Overall b value: 150 / Ref protocol: RIGID BODY FIT / Ref space: REAL
Atomic model buildingPDB-ID: 4C2M
Least-squares processHighest resolution: 4.8 Å
Refine hist #LASTHighest resolution: 4.8 Å
Number of atoms included #LASTProtein: 37342 / Nucleic acid: 0 / Ligand: 7 / Solvent: 0 / Total: 37349

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