← Back to search
9dum

Human PELP1-WDR18-TEX10 complex

Method: ELECTRON MICROSCOPY Dmax: 159.9 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

WD repeat-containing protein 18

Homo sapiens

UniProt Q9BV38

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–432 Chain B； UniProt 1–432 Not recorded Proline-, glutamic acid- and leucine-rich protein 1 × 2 （Q8IZL8） Testis-expressed protein 10 × 2 （Q9NXF1） ELECTRON MICROSCOPY cryo-EM buffer：pH 8；20mM Hepes pH8.0, 400mM NaCl, 5mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.56 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 9DUM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7UWF Human Rix1 sub-complex scaffold Deposited 2022-05-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–432（432 aa）
Chain B 1–432（432 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8FL2 Human nuclear pre-60S ribosomal subunit (State I1) Deposited 2022-12-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 65-meric
Chain NV 1–432（432 aa）
Chain NW 1–432（432 aa）
Not recorded MG MAGNESIUM ION × 100 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.67 Å
8FL3 Human nuclear pre-60S ribosomal subunit (State I2) Deposited 2022-12-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 60 PDB declaration: 63-meric
Chain NV 1–432（432 aa）
Chain NW 1–432（432 aa）
Not recorded MG MAGNESIUM ION × 100 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.53 Å
8FL4 Human nuclear pre-60S ribosomal subunit (State I3) Deposited 2022-12-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 62-meric
Chain NV 1–432（432 aa）
Chain NW 1–432（432 aa）
Not recorded MG MAGNESIUM ION × 99 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.89 Å
9DUO Human PELP1-WDR18 complex Deposited 2024-10-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–432（432 aa）
Chain B 1–432（432 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20mM Hepes pH8.0, 250mM NaCl, 5mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WDR18_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–434； UniProt 1–432 Author chain B； PDBConstruct 3–434； UniProt 1–432

Proline-, glutamic acid- and leucine-rich protein 1

Homo sapiens

UniProt Q8IZL8

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain C； UniProt 1–642 Chain D； UniProt 1–642 Not recorded WD repeat-containing protein 18 × 2 （Q9BV38） Testis-expressed protein 10 × 2 （Q9NXF1） ELECTRON MICROSCOPY cryo-EM buffer：pH 8；20mM Hepes pH8.0, 400mM NaCl, 5mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.56 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 9DUM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8FL2 Human nuclear pre-60S ribosomal subunit (State I1) Deposited 2022-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 65-meric
Chain NX 1–1130（1130 aa）
Chain NY 1–1130（1130 aa）
Not recorded MG MAGNESIUM ION × 100 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.67 Å
8FL3 Human nuclear pre-60S ribosomal subunit (State I2) Deposited 2022-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 60 PDB declaration: 63-meric
Chain NX 1–1130（1130 aa）
Chain NY 1–1130（1130 aa）
Not recorded MG MAGNESIUM ION × 100 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.53 Å
8FL4 Human nuclear pre-60S ribosomal subunit (State I3) Deposited 2022-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 62-meric
Chain NX 1–1130（1130 aa）
Chain NY 1–1130（1130 aa）
Not recorded MG MAGNESIUM ION × 99 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.89 Å
9DUO Human PELP1-WDR18 complex Deposited 2024-10-03 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–642（642 aa）
Chain D 1–642（642 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20mM Hepes pH8.0, 250mM NaCl, 5mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
9ME8 Co-crystal structure of maltose binding protein (MBP)-human SENP3 fusion protein in complex with PELP1 peptide Deposited 2024-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 764–781（18 aa）
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.085M HEPES pH 7.5, 17-20% (v/v) PEG8000
Resolution 2.93 Å R-free 0.232

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PELP1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 3–644； UniProt 1–642 Author chain D； PDBConstruct 3–644； UniProt 1–642

Testis-expressed protein 10

Homo sapiens

UniProt Q9NXF1

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain G； UniProt 1–929 Chain H； UniProt 1–929 Not recorded WD repeat-containing protein 18 × 2 （Q9BV38） Proline-, glutamic acid- and leucine-rich protein 1 × 2 （Q8IZL8） ELECTRON MICROSCOPY cryo-EM buffer：pH 8；20mM Hepes pH8.0, 400mM NaCl, 5mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.56 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 9DUM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8FL2 Human nuclear pre-60S ribosomal subunit (State I1) Deposited 2022-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 65-meric
Chain NU 1–929（929 aa）
Not recorded MG MAGNESIUM ION × 100 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.67 Å
8FL3 Human nuclear pre-60S ribosomal subunit (State I2) Deposited 2022-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 60 PDB declaration: 63-meric
Chain NU 1–929（929 aa）
Not recorded MG MAGNESIUM ION × 100 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.53 Å
8FL4 Human nuclear pre-60S ribosomal subunit (State I3) Deposited 2022-12-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 62-meric
Chain NU 1–929（929 aa）
Not recorded MG MAGNESIUM ION × 99 ZN ZINC ION × 5 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 K POTASSIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE；Four applications with manual blotting before last blotting with the vitrobot.
Resolution 2.89 Å

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

View Construct and Data Evidence
UniProt name TEX10_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain G； PDBConstruct 3–931； UniProt 1–929 Author chain H； PDBConstruct 3–931； UniProt 1–929

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 9dum

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9dum
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id9dum
Deposition date deposition_date2024-10-03
Structure title titleHuman PELP1-WDR18-TEX10 complex
Keywords keywordsComplex, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier50.02 Å
Radius of gyration Rg (electron density) rg_electron49.90 Å
Forward intensity I(0) i01410420000.00
Molecular weight molecular_weight322610.0 kDa
Excluded volume excluded_volume408380 ų
Envelope volume envelope_volume603680 ų
Hydration-shell volume shell_volume98822 ų
Envelope diameter envelope_diameter163.5 Å
Shell Rg shell_rg55.72 Å
Envelope Rg envelope_rg48.81 Å
Shape Rg shape_rg49.89 Å
Total Rg total_rg50.13 Å
Total atoms total_atoms22662
Residues n_residues2915
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax159.9 Å
Rg (real space) rg_real49.85 Å
Rg uncertainty (real space) rg_real_error1.72 Å
I(0) (real space) i0_real1.4100e+09
I(0) uncertainty (real space) i0_real_error2.9850e+07
Rg (reciprocal space) rg_reciprocal50.14 Å
I(0) (reciprocal space) i0_reciprocal1411000000.0000
Solution quality estimate total_estimate0.8920
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary61.9 Å
Skewness Skewness skewness0.125
Kurtosis Kurtosis kurtosis-0.535
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha142400000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.922; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.840
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▶

8. Citations (1)

▶

9. Files and Curves (10)