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2mvf

Structural insight into an essential assembly factor network on the pre-ribosome

Method: SOLUTION NMR Dmax: 50.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Uncharacterized protein

Chaetomium thermophilum

UniProt G0S081

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 168–261 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7.4；280 K；Ionic strength (raw mmCIF value) 5；Pressure ambient NMR sample composition：10 % D2O, 10 mM TRIS, 90 % H2O, 5 mM sodium chloride, 1 uM DSS, 2 mM TCEP, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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 2MVF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8I9T Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-1 Deposited 2023-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8I9V Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-2 Deposited 2023-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8I9W Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Dbp10-3 Deposited 2023-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 52-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8I9X Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-1 Deposited 2023-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 60-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8I9Y Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-2 Deposited 2023-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 59-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8I9Z Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Spb4 Deposited 2023-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 60-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8IA0 Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Puf6 Deposited 2023-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 62 PDB declaration: 64-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8PV1 Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - composite structure Deposited 2023-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.56 Å
8PV2 Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 Deposited 2023-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.63 Å
8PV3 Chaetomium thermophilum pre-60S State 9 - pre-5S rotation - immature H68/H69 - composite structure Deposited 2023-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8PV4 Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - composite structure Deposited 2023-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 62 PDB declaration: 66-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8PV5 Chaetomium thermophilum pre-60S State 8 - pre-5S rotation without Foot - composite structure Deposited 2023-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
8PV6 Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - composite structure Deposited 2023-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 60 PDB declaration: 64-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
8PV7 Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - Composite structure Deposited 2023-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 59-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.12 Å
8PV8 Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - composite structure Deposited 2023-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
8PVK Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - composite structure Deposited 2023-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 60-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.55 Å
8PVL Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - composite structure Deposited 2023-07-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 58-meric
Chain CK 1–261（261 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.19 Å

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name G0S081_CHATD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–94； UniProt 168–261

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 2mvf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2mvf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2mvf
Deposition date deposition_date2014-10-02
Structure title titleStructural insight into an essential assembly factor network on the pre-ribosome
Keywords keywordsRIBOSOME BIOGENESIS, RIBOSOMAL PROTEIN; RIBOSOMAL PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.06 Å
Radius of gyration Rg (electron density) rg_electron14.04 Å
Forward intensity I(0) i0537786000.00
Molecular weight molecular_weight205900.0 kDa
Excluded volume excluded_volume262390 ų
Envelope volume envelope_volume30479 ų
Hydration-shell volume shell_volume15486 ų
Envelope diameter envelope_diameter58.8 Å
Shell Rg shell_rg22.61 Å
Envelope Rg envelope_rg17.14 Å
Shape Rg shape_rg14.04 Å
Total Rg total_rg14.25 Å
Total atoms total_atoms29700
Residues n_residues1880
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 dmax50.6 Å
Rg (real space) rg_real14.07 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real5.3780e+08
I(0) uncertainty (real space) i0_real_error6.5730e+06
Rg (reciprocal space) rg_reciprocal14.07 Å
I(0) (reciprocal space) i0_reciprocal537800000.0000
Solution quality estimate total_estimate0.7373
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary16.0 Å
Skewness Skewness skewness0.388
Kurtosis Kurtosis kurtosis-0.005
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha232000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.543; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)