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Yorodumi- EMDB-8772: Core Factor local refinement from Pol I Initial Transcribing Comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8772 | ||||||||||||||||||
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Title | Core Factor local refinement from Pol I Initial Transcribing Complex at 4.2 angstrom | ||||||||||||||||||
Map data | Core Factor local refinement from Pol I Initial Transcribing Complex | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / TBP-class protein binding / nucleolus ...RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / TBP-class protein binding / nucleolus / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||||||||||||||
Authors | Han Y / He Y | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Elife / Year: 2017 Title: Structural mechanism of ATP-independent transcription initiation by RNA polymerase I. Authors: Yan Han / Chunli Yan / Thi Hoang Duong Nguyen / Ashleigh J Jackobel / Ivaylo Ivanov / Bruce A Knutson / Yuan He / Abstract: Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a ...Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Pol I-CF-DNA to 3.8 Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8772.map.gz | 1.3 MB | EMDB map data format | |
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Header (meta data) | emd-8772-v30.xml emd-8772.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8772_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_8772.png | 214.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8772 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8772 | HTTPS FTP |
-Validation report
Summary document | emd_8772_validation.pdf.gz | 78.6 KB | Display | EMDB validaton report |
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Full document | emd_8772_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_8772_validation.xml.gz | 495 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8772 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8772 | HTTPS FTP |
-Related structure data
Related structure data | 8771C 8773C 8774C 8775C 8776C 8777C 5w5yC 5w64C 5w65C 5w66C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8772.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Core Factor local refinement from Pol I Initial Transcribing Complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Yeast Core Factor
Entire | Name: Yeast Core Factor |
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Components |
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-Supramolecule #1: Yeast Core Factor
Supramolecule | Name: Yeast Core Factor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Molecular weight | Theoretical: 250 KDa |
-Macromolecule #1: Rrn7
Macromolecule | Name: Rrn7 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSTFIRGPIC GTDNCPSRLW RIIDGRRTCQ YGHVMEGDVE FNDDEDDLNG LGAGVITRRL NLTTNATGS FQSSQLTNSQ LLQQQQRQSH KKFKKLIGHE AKLLFLKSFQ FILKRQIRWL I TEMRFPKE FEHVAKIIWL KILKTINDQP QEELKLQLHM TSTISILYLA ...String: MSTFIRGPIC GTDNCPSRLW RIIDGRRTCQ YGHVMEGDVE FNDDEDDLNG LGAGVITRRL NLTTNATGS FQSSQLTNSQ LLQQQQRQSH KKFKKLIGHE AKLLFLKSFQ FILKRQIRWL I TEMRFPKE FEHVAKIIWL KILKTINDQP QEELKLQLHM TSTISILYLA STHLSLPVYT CD YIKWICT AKMPYFQASE ILPKSWRIQL PNYYVSILEG SISPFNGQLY NKIALTCGMI HFK EFFNSE ISCQGLLLKL VMQCALPPEF YFYTKQVIEF EETDIRNLTL WERTDERHTG RVSN HAELR VLSYFMLTIN WMLSFDRDRQ YPLKWILSLT ESLTQRTTTS ESIGRNIVKV VYPDK PTSS DYFQWSEEET LEFLKWMEKQ FLPTQTKSLH NENGSMEMTI DQKIARRKLY KIFPLD REA NHDGEFNDST HQLTFIEDLQ ERYAKQTPFF ESNKIRDSLN YQEANPPARK EAIGRLL TH IASQLLVDFA ISKEQLKDCI SRIKNACLHR MN |
-Macromolecule #2: Rrn11
Macromolecule | Name: Rrn11 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MFEVPITLTN RKFAQRRKLK YQYINYISRR FDRISKKSTT TDSLPTPENS AAENNDEEEG QNSEAGTYR RSVLQQKKRR RERHWRSVVG EIYSTTESET DSQEEETEEG GEHDTGIDKE D SDEERKFW KKYEKPEKSF EIWRTVSSQN KQPINKQKMT YHNFKKIEKI ...String: MFEVPITLTN RKFAQRRKLK YQYINYISRR FDRISKKSTT TDSLPTPENS AAENNDEEEG QNSEAGTYR RSVLQQKKRR RERHWRSVVG EIYSTTESET DSQEEETEEG GEHDTGIDKE D SDEERKFW KKYEKPEKSF EIWRTVSSQN KQPINKQKMT YHNFKKIEKI PLRKMEIPLL HC TKENKLY FQSISRGLEP LKTSTSEVRN YRTRHIVTLT DLLHLNVSRH NWSLAYKIFA TLI RIPGVQ IKSLWGIGVE ILDNLSNSSS GLDFLQWMCQ IYSSKSRFVQ NINYRSIVPP FQTG SRTHT AKFAITYLWS SLINCQKSME PSSNIIDKPF DTENDLLQEL IDKISEWVLT PPFME DAEV WFIYASCHLL KADTLSRQFV NDNKNNDLIG LDRDIKINQV IKHIHYVRTF LKICLD KGG FAVPSRLIEN QLKSFESRLY GEAQDIQERD VANVYDSIDN SSVENSFGDV YETNAEF LD TQLMDLSPED NGLDEMHYSD EDSSE |
-Macromolecule #3: Rrn6
Macromolecule | Name: Rrn6 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSEGQIPSSD VLGSQLGVGV QGASLYCPQE NYTTKKQEKP QWLRPVDDTL AEDALDLHIV VKSLLCDTA IRYISDDKVL QESDADDDLI TSDIDEDTDN QGDTSIVVNP VIPVVPKDVH F FKKVDVGN DSMFGVNCDT PVSFQDYIPS DLLRNLDDTL QESTNSSRPM ...String: MSEGQIPSSD VLGSQLGVGV QGASLYCPQE NYTTKKQEKP QWLRPVDDTL AEDALDLHIV VKSLLCDTA IRYISDDKVL QESDADDDLI TSDIDEDTDN QGDTSIVVNP VIPVVPKDVH F FKKVDVGN DSMFGVNCDT PVSFQDYIPS DLLRNLDDTL QESTNSSRPM QDAFFWDPTV AN RLDSQYI QTASDLRNYR DGTEIIAYAS GKTGSVLNIA VLTRQNTLHL NRHNNVTSIE LHS PIKSIK IPGASESIGR RSNLVGIITE NSFQIFRIES VHSRSCDVMV SSSEPLYFVE IDDL QVVDF AFNPWDLQQF AIIDIKGNWS IGRIPKNFNN NNKRKLQLID NLHGTIFDPE ELSSW KRIE WFSHFQKILV FDRSKMIEID FMNNWQTEVV QAKAWSNIRD YKRIDDKNGI LLTSRE III VGASESNDPV RRISWKHDLD PDDTTLRITV QKVKKPDHIL LVAFVYSMRH KRIYMHV FS HRKANLFQSL GCSTVLEIPG GTPTGIETIL TLDHIDDESR REEDADENFE LVVDFLVK L RNSSEVYYYA LSNTQNSEPN KQETPIIVDH PEWASLFNNA DEREKESIGA LVSQIKLKE RERISRVQNL IEHENSHDED KYLQDLGYRL SIATNELLES WQKTKDESIL SGSLSHSKLK NLLENSDSF ASIPEFSSLL DQFFQYYQDQ DVTFIGFEKL LHLFLHEDVP GLDIFYNKLL Q CWVLVSPQ AELLTKEIVK DIIWSLARLE KPSLFEPIQN EISRSLSGPY QDIISSWDMD DI NEEDESN EFNFDSQFSA PFNGRPPFNL NSQSQIPTIK SSQSSGLARR KRILKTQSQK ATP LSQSTQ NLSVLPDSMT PAFTLMQPPS SQISFVNDSQ PRNSQKAKKK KKRIRGFG |
-Macromolecule #4: non-template strand DNA
Macromolecule | Name: non-template strand DNA / type: dna / ID: 4 / Classification: DNA |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Sequence | String: CAAGTGTGAG GAAAAGTAGT TGGGTTTTTT TTTTTTTTTT TGCAGTTGAA GACA |
-Macromolecule #5: template DNA
Macromolecule | Name: template DNA / type: dna / ID: 5 / Classification: DNA |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) |
Sequence | String: TGTCTTCAAC TGCTTTCGCA TGAAGTACCT CCCAACTACT TTTCCTCACA CTTG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil S7/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 12.0 sec. / Average electron dose: 56.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 4.5 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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