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- EMDB-21540: Holocomplex of E. coli class Ia ribonucleotide reductase with GDP... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21540 | |||||||||
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Title | Holocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP | |||||||||
![]() | Holocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP | |||||||||
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Function / homology | ![]() ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / DNA replication / iron ion binding ...ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / ribonucleoside-diphosphate reductase complex / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / protein folding chaperone / DNA replication / iron ion binding / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Kang G / Taguchi A / Stubbe J / Drennan C | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a trapped radical transfer pathway within a ribonucleotide reductase holocomplex. Authors: Gyunghoon Kang / Alexander T Taguchi / JoAnne Stubbe / Catherine L Drennan / ![]() Abstract: Ribonucleotide reductases (RNRs) are a diverse family of enzymes that are alone capable of generating 2'-deoxynucleotides de novo and are thus critical in DNA biosynthesis and repair. The nucleotide ...Ribonucleotide reductases (RNRs) are a diverse family of enzymes that are alone capable of generating 2'-deoxynucleotides de novo and are thus critical in DNA biosynthesis and repair. The nucleotide reduction reaction in all RNRs requires the generation of a transient active site thiyl radical, and in class I RNRs, this process involves a long-range radical transfer between two subunits, α and β. Because of the transient subunit association, an atomic resolution structure of an active α2β2 RNR complex has been elusive. We used a doubly substituted β2, E52Q/(2,3,5)-trifluorotyrosine122-β2, to trap wild-type α2 in a long-lived α2β2 complex. We report the structure of this complex by means of cryo-electron microscopy to 3.6-angstrom resolution, allowing for structural visualization of a 32-angstrom-long radical transfer pathway that affords RNR activity. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.6 KB 19.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.6 KB | Display | ![]() |
Images | ![]() | 77.8 KB | ||
Others | ![]() ![]() | 40.8 MB 40.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 820.4 KB | Display | ![]() |
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Full document | ![]() | 820 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 20 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6w4xMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Holocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_21540_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_21540_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Holocomplex of E. coli class Ia ribonucleotide reductase with GDP...
Entire | Name: Holocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP |
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Components |
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-Supramolecule #1: Holocomplex of E. coli class Ia ribonucleotide reductase with GDP...
Supramolecule | Name: Holocomplex of E. coli class Ia ribonucleotide reductase with GDP and TTP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Ribonucleoside-diphosphate reductase 1 subunit alpha
Macromolecule | Name: Ribonucleoside-diphosphate reductase 1 subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonucleoside-diphosphate reductase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 85.877086 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNQNLLVTKR DGSTERINLD KIHRVLDWAA EGLHNVSISQ VELRSHIQFY DGIKTSDIHE TIIKAAADLI SRDAPDYQYL AARLAIFHL RKKAYGQFEP PALYDHVVKM VEMGKYDNHL LEDYTEEEFK QMDTFIDHDR DMTFSYAAVK QLEGKYLVQN R VTGEIYES ...String: MNQNLLVTKR DGSTERINLD KIHRVLDWAA EGLHNVSISQ VELRSHIQFY DGIKTSDIHE TIIKAAADLI SRDAPDYQYL AARLAIFHL RKKAYGQFEP PALYDHVVKM VEMGKYDNHL LEDYTEEEFK QMDTFIDHDR DMTFSYAAVK QLEGKYLVQN R VTGEIYES AQFLYILVAA CLFSNYPRET RLQYVKRFYD AVSTFKISLP TPIMSGVRTP TRQFSSCVLI ECGDSLDSIN AT SSAIVKY VSQRAGIGIN AGRIRALGSP IRGGEAFHTG CIPFYKHFQT AVKSCSQGGV RGGAATLFYP MWHLEVESLL VLK NNRGVE GNRVRHMDYG VQINKLMYTR LLKGEDITLF SPSDVPGLYD AFFADQEEFE RLYTKYEKDD SIRKQRVKAV ELFS LMMQE RASTGRIYIQ NVDHCNTHSP FDPAIAPVRQ SNLCLEIALP TKPLNDVNDE NGEIALCTLS AFNLGAINNL DELEE LAIL AVRALDALLD YQDYPIPAAK RGAMGRRTLG IGVINFAYYL AKHGKRYSDG SANNLTHKTF EAIQYYLLKA SNELAK EQG ACPWFNETTY AKGILPIDTY KKDLDTIANE PLHYDWEALR ESIKTHGLRN STLSALMPSE TSSQISNATN GIEPPRG YV SIKASKDGIL RQVVPDYEHL HDAYELLWEM PGNDGYLQLV GIMQKFIDQS ISANTNYDPS RFPSGKVPMQ QLLKDLLT A YKFGVKTLYY QNTRDGAEDA QDDLVPSIQD DGCESGACKI |
-Macromolecule #2: Ribonucleoside-diphosphate reductase 1 subunit beta
Macromolecule | Name: Ribonucleoside-diphosphate reductase 1 subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribonucleoside-diphosphate reductase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 43.611039 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAYTTFSQTK NDQLKEPMFF GQPVNVARYD QQKYDIFEKL IEKQLSFFWR PEQVDVSRDR IDYQALPEHE KHIFISNLKY QTLLDSIQG RSPNVALLPL ISIPELETWV ETWAFSETIH SRS(FY3)THIIRN IVNDPSVVFD DIVTNEQIQK RAEGISS YY DELIEMTSYW ...String: MAYTTFSQTK NDQLKEPMFF GQPVNVARYD QQKYDIFEKL IEKQLSFFWR PEQVDVSRDR IDYQALPEHE KHIFISNLKY QTLLDSIQG RSPNVALLPL ISIPELETWV ETWAFSETIH SRS(FY3)THIIRN IVNDPSVVFD DIVTNEQIQK RAEGISS YY DELIEMTSYW HLLGEGTHTV NGKTVTVSLR ELKKKLYLCL MSVNALEAIR FYVSFACSFA FAERELMEGN AKIIRLIA R DEALHLTGTQ HMLNLLRSGA DDPEMAEIAE ECKQECYDLF VQAAQQEKDW ADYLFRDGSM IGLNKDILCQ YVEYITNIR MQAVGLDLPF QTRSNPIPWI NTWLVSDNVQ VAPQEVEVSS YLVGQIDSEV DTDDLSNFQL |
-Macromolecule #3: THYMIDINE-5'-TRIPHOSPHATE
Macromolecule | Name: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: TTP |
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Molecular weight | Theoretical: 482.168 Da |
Chemical component information | ![]() ChemComp-TTP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ![]() ChemComp-GDP: |
-Macromolecule #6: MU-OXO-DIIRON
Macromolecule | Name: MU-OXO-DIIRON / type: ligand / ID: 6 / Number of copies: 2 / Formula: FEO |
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Molecular weight | Theoretical: 127.689 Da |
Chemical component information | ![]() ChemComp-FEO: |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 4 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 4.5 seconds before plunging. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 2 / Number real images: 6238 / Average exposure time: 6.0 sec. / Average electron dose: 47.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |