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8yf5

Cryo EM structure of Komagataella phaffii Rat1-Rai1-Rtt103 complex

Method: ELECTRON MICROSCOPY Dmax: 162.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

;5'-3' exoribonuclease ;

Komagataella phaffii

UniProt F2QV79

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain A； UniProt 1–994 Chain C； UniProt 1–994 Mutation：D233A, D235A Decapping nuclease × 2 （F2QLF5） Exonuclease Rat1p and Rai1p interacting protein × 1 （F2QNA8） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；EMGP2 Resolution 3.78 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8YF5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8YFE Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex Deposited 2024-02-24 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–994（994 aa）
Chain C 1–994（994 aa）
Mutation：D233A, D235A Mutation：D233A, D235A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.47 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain R 1–994（994 aa）
Mutation：E203Q, E205Q, D233N, D235N, D330N ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain R 1–994（994 aa）
Mutation：E203Q, E205Q, D233N, D235N, D330N ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.40 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F2QV79_KOMPC
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–994； UniProt 1–994 Author chain C； PDBConstruct 1–994； UniProt 1–994

Decapping nuclease

Komagataella phaffii

UniProt F2QLF5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain B； UniProt 1–381 Chain D； UniProt 1–381 Mutation：E213A, D215A ;5'-3' exoribonuclease ; × 2 （F2QV79） Exonuclease Rat1p and Rai1p interacting protein × 1 （F2QNA8） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；EMGP2 Resolution 3.78 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8YF5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8YFE Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex Deposited 2024-02-24 Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–381（381 aa）
Chain D 1–381（381 aa）
Mutation：E213A, D215A,D233N Mutation：E213A, D215A,D233N No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.47 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain S 1–381（381 aa）
Mutation：E213A, D215A ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain S 1–381（381 aa）
Mutation：E213A, D215A ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.40 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F2QLF5_KOMPC
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 4–384； UniProt 1–381 Author chain D； PDBConstruct 4–384； UniProt 1–381

Exonuclease Rat1p and Rai1p interacting protein

Komagataella phaffii

UniProt F2QNA8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count Chain E； UniProt 1–375 Not recorded ;5'-3' exoribonuclease ; × 2 （F2QV79） Decapping nuclease × 2 （F2QLF5） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；EMGP2 Resolution 3.78 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name F2QNA8_KOMPC
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E； PDBConstruct 1–375； UniProt 1–375

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8yf5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8yf5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8yf5
Deposition date deposition_date2024-02-24
Structure title titleCryo EM structure of Komagataella phaffii Rat1-Rai1-Rtt103 complex
Keywords keywordstranscription termination, RNA polymerase II, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier49.18 Å
Radius of gyration Rg (electron density) rg_electron48.54 Å
Forward intensity I(0) i0951084000.00
Molecular weight molecular_weight261670.0 kDa
Excluded volume excluded_volume329750 ų
Envelope volume envelope_volume466780 ų
Hydration-shell volume shell_volume80254 ų
Envelope diameter envelope_diameter157.9 Å
Shell Rg shell_rg52.27 Å
Envelope Rg envelope_rg47.34 Å
Shape Rg shape_rg48.52 Å
Total Rg total_rg48.75 Å
Total atoms total_atoms18476
Residues n_residues2250
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax162.5 Å
Rg (real space) rg_real49.01 Å
Rg uncertainty (real space) rg_real_error1.32 Å
I(0) (real space) i0_real9.5110e+08
I(0) uncertainty (real space) i0_real_error1.6960e+07
Rg (reciprocal space) rg_reciprocal49.18 Å
I(0) (reciprocal space) i0_reciprocal951300000.0000
Solution quality estimate total_estimate0.8981
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary60.9 Å
Skewness Skewness skewness0.171
Kurtosis Kurtosis kurtosis-0.601
Angular range angular_range— – 0.1600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha147700000.0000
Real-space data points n_real_points33
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.934
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)