SAXSdb — 9duo

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

WD repeat-containing protein 18

Homo sapiens

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 × 4 PDB declaration: tetrameric（4） 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）	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

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 9DUO	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 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
9DUM Human PELP1-WDR18-TEX10 complex Deposited 2024-10-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	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, 400mM NaCl, 5mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–642 Chain D； UniProt 1–642	Not recorded	WD repeat-containing protein 18 × 2 （Q9BV38）	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

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 9DUO	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
9DUM Human PELP1-WDR18-TEX10 complex Deposited 2024-10-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	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, 400mM NaCl, 5mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.56 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

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9duo
Deposition date deposition_date	2024-10-03
Structure title title	Human PELP1-WDR18 complex
Keywords keywords	Complex, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	37.19 Å
Radius of gyration Rg (electron density) rg_electron	36.32 Å
Forward intensity I(0) i0	522526000.00
Molecular weight molecular_weight	188160.0 kDa
Excluded volume excluded_volume	236720 Å³
Envelope volume envelope_volume	300830 Å³
Hydration-shell volume shell_volume	66593 Å³
Envelope diameter envelope_diameter	109.4 Å
Shell Rg shell_rg	44.99 Å
Envelope Rg envelope_rg	35.53 Å
Shape Rg shape_rg	36.33 Å
Total Rg total_rg	36.82 Å
Total atoms total_atoms	13187
Residues n_residues	1736
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	112.5 Å
Rg (real space) rg_real	36.93 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	5.2250e+08
I(0) uncertainty (real space) i0_real_error	8.4240e+06
Rg (reciprocal space) rg_reciprocal	37.10 Å
I(0) (reciprocal space) i0_reciprocal	522600000.0000
Solution quality estimate total_estimate	0.8338
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.7 Å
Skewness Skewness skewness	0.073
Kurtosis Kurtosis kurtosis	-0.609
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	106300000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	WD repeat-containing protein 18
Molecular weight formula_weight	47660.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	13187

SNMAAPMEVAVCTDSAAPMWSCIVWELHSGANLLTYRGGQAGPRGLALLNGEYLLAAQLGKNYISAWELQRKDQLQQKIMCPGPVTCLTASPNGLYVLAGVAESIHLWEVSTGNLLVILSRHYQDVSCLQFTGDSSHFISGGKDCLVLVWSLCSVLQADPSRIPAPRHVWSHHALPITDLHCGFGGPLARVATSSLDQTVKLWEVSSGELLLSVLFDVSIMAVTMDLAEHHMFCGGSEGSIFQVDLFTWPGQRERSFHPEQDAGKVFKGHRNQVTCLSVSTDGSVLLSGSHDETVRLWDVQSKQCIRTVALKGPVTNAAILLAPVSMLSSDFRPSLPLPHFNKHLLGAEHGDEPRHGGLTLRLGLHQQGSEPSYLDRTEQLQAVLCSTMEKSVLGGQDQLRVRVTELEDEVRNLRKINRDLFDFSTRFITRPAK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Proline-, glutamic acid- and leucine-rich protein 1
Molecular weight formula_weight	68266.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

SNMAAAVLSGPSAGSAAGVPGGTGGLSAVSSGPRLRLLLLESVSGLLQPRTGSAVAPVHPPNRSAPHLPGLMCLLRLHGSVGGAQNLSALGALVSLSNARLSSIKTRFEGLCLLSLLVGESPTELFQQHCVSWLRSIQQVLQTQDPPATMELAVAVLRDLLRYAAQLPALFRDISMNHLPGLLTSLLGLRPECEQSALEGMKACMTYFPRACGSLKGKLASFFLSRVDALSPQLQQLACECYSRLPSLGAGFSQGLKHTESWEQELHSLLASLHTLLGALYEGAETAPVQNEGPGVEMLLSSEDGDAHVLLQLRQRFSGLARCLGLMLSSEFGAPVSVPVQEILDFICRTLSVSSKNISLHGDGPLRLLLLPSIHLEALDLLSALILACGSRLLRFGILIGRLLPQVLNSWSIGRDSLSPGQERPYSTVRTKVYAILELWVQVCGASAGMLQGGASGEALLTHLLSDISPPADALKLRSPRGSPDGSLQTGKPSAPKKLKLDVGEAMAPPSHRKGDSNANSDVCAAALRGLSRTILMCGPLIKEETHRRLHDLVLPLVMGVQQGEVLGSSPYTSSRCRRELYCLLLALLLAPSPRCPPPLACALQAFSLGQREDSLEVSSFCSEALVTCAALTHPRVPPLQPMG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.66 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	1076956

fit	/app/data/saxs_computation/du/9duo/9duo.fit
pddf	/app/data/pr_computation/du/9duo/9duo.pr.out
profile	/app/data/saxs_computation/du/9duo/9duo.dat

Human PELP1-WDR18 complex

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

WD repeat-containing protein 18

State in the Current Structure

Other States of the Same Protein in the Database

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

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)