SAXSdb — 4yoo

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

Retinoblastoma-like protein 1,Retinoblastoma-like protein 1

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 391–600 Chain A； UniProt 781–972	Fragment：unp residues 391-600,unp residues 781-972	LIN52 peptide × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；MES, PEG 400 4%, 1.6M ammonium sulfate	Resolution 2.40 Å R-free 0.242

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 4YOO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H28 CDK2/CyclinA in complex with an 11-residue recruitment peptide from p107 Deposited 2002-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 653–663（11 aa） Fragment：RB PEPTIDE, RESIDUES 653-663	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.8M KCL, 1.2M (NH4)2SO4, 40MM HEPES PH 7.0. PROTEIN CONCENTRATION = 10MG/ML	Resolution 2.80 Å R-free 0.323
1H28 CDK2/CyclinA in complex with an 11-residue recruitment peptide from p107 Deposited 2002-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 653–663（11 aa） Fragment：RB PEPTIDE, RESIDUES 653-663	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.8M KCL, 1.2M (NH4)2SO4, 40MM HEPES PH 7.0. PROTEIN CONCENTRATION = 10MG/ML	Resolution 2.80 Å R-free 0.323
4YOS p107 pocket domain complexed with LIN52 peptide Deposited 2015-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 391–600（210 aa） Fragment：unp residues 391-600,unp residues 781-969,unp residues 391-600,unp residues 781-969	Not recorded	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；MES, PEG 400 4%, 1.6M ammonium sulfate	Resolution 2.30 Å R-free 0.242
4YOZ p107 pocket domain in complex with HPV E7 peptide Deposited 2015-03-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 391–593（203 aa） Fragment：unp residues 391-593,unp residues 391-593 Chain A 777–972（196 aa） Fragment：unp residues 391-593,unp residues 391-593	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；Hepes, Ammonium Sulfate, PEG 400	Resolution 2.25 Å R-free 0.240
5TUV Crystal structure of the E2F5-DP1-p107 ternary complex Deposited 2016-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 994–1031（38 aa） Fragment：UNP residues 994-1031	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100mM Hepes pH 7.0, 7% PEG 5000, 5% 1-propanol, 2% 2-propanol	Resolution 2.90 Å R-free 0.260
5TUV Crystal structure of the E2F5-DP1-p107 ternary complex Deposited 2016-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 994–1031（38 aa） Fragment：UNP residues 994-1031	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100mM Hepes pH 7.0, 7% PEG 5000, 5% 1-propanol, 2% 2-propanol	Resolution 2.90 Å R-free 0.260
5TUV Crystal structure of the E2F5-DP1-p107 ternary complex Deposited 2016-11-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 994–1031（38 aa） Fragment：UNP residues 994-1031 Chain F 994–1031（38 aa） Fragment：UNP residues 994-1031	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100mM Hepes pH 7.0, 7% PEG 5000, 5% 1-propanol, 2% 2-propanol	Resolution 2.90 Å R-free 0.260
7SMC p107 pocket domain complexed with ARID4A peptide Deposited 2021-10-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 391–601（211 aa） Fragment：UNP residues 391-601,780-887,924-972 Chain A 780–887（108 aa） Fragment：UNP residues 391-601,780-887,924-972 Chain A 924–972（49 aa） Fragment：UNP residues 391-601,780-887,924-972	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate	Resolution 2.70 Å R-free 0.298
7SMC p107 pocket domain complexed with ARID4A peptide Deposited 2021-10-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 391–601（211 aa） Fragment：UNP residues 391-601,780-887,924-972 Chain C 780–887（108 aa） Fragment：UNP residues 391-601,780-887,924-972 Chain C 924–972（49 aa） Fragment：UNP residues 391-601,780-887,924-972	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate	Resolution 2.70 Å R-free 0.298
7SMD p107 pocket domain complexed with EID1 peptide Deposited 2021-10-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 391–601（211 aa） Fragment：UNP residues 391-601,780-887,924-972 Chain A 780–887（108 aa） Fragment：UNP residues 391-601,780-887,924-972 Chain A 924–972（49 aa） Fragment：UNP residues 391-601,780-887,924-972	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate	Resolution 2.15 Å R-free 0.259
7SME p107 pocket domain complexed with HDAC1 peptide Deposited 2021-10-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 391–601（211 aa） Fragment：UNP residues 391-601,780-887,924-972 Chain A 780–887（108 aa） Fragment：UNP residues 391-601,780-887,924-972 Chain A 924–972（49 aa） Fragment：UNP residues 391-601,780-887,924-972	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate	Resolution 2.64 Å R-free 0.277
7SMF p107 pocket domain complexed with mutated HDAC1-3X peptide Deposited 2021-10-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 391–601（211 aa） Fragment：UNP residues 391-601,780-887,924-972 Chain A 780–887（108 aa） Fragment：UNP residues 391-601,780-887,924-972 Chain A 924–972（49 aa） Fragment：UNP residues 391-601,780-887,924-972	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate	Resolution 3.00 Å R-free 0.301
7SMF p107 pocket domain complexed with mutated HDAC1-3X peptide Deposited 2021-10-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 391–601（211 aa） Fragment：UNP residues 391-601,780-887,924-972 Chain C 780–887（108 aa） Fragment：UNP residues 391-601,780-887,924-972 Chain C 924–972（49 aa） Fragment：UNP residues 391-601,780-887,924-972	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate	Resolution 3.00 Å R-free 0.301
9C6B PP2A:B55-p107 substrate complex Deposited 2024-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 612–687（76 aa） Fragment：residues 612-687	Not recorded	FE2 FE (II) ION × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å

9 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RBL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–213； UniProt 391–600 Author chain A； PDBConstruct 214–369； UniProt 781–972

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	4yoo
Deposition date deposition_date	2015-03-12
Structure title title	p107 pocket domain in complex with LIN52 P29A peptide
Keywords keywords	Cyclin Box Pocket Protein Transcriptional Regulator Cell Cycle, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	23.99 Å
Radius of gyration Rg (electron density) rg_electron	23.06 Å
Forward intensity I(0) i0	29371900.00
Molecular weight molecular_weight	42099.0 kDa
Excluded volume excluded_volume	52923 Å³
Envelope volume envelope_volume	63422 Å³
Hydration-shell volume shell_volume	23311 Å³
Envelope diameter envelope_diameter	80.3 Å
Shell Rg shell_rg	29.61 Å
Envelope Rg envelope_rg	23.19 Å
Shape Rg shape_rg	23.03 Å
Total Rg total_rg	23.96 Å
Total atoms total_atoms	2954
Residues n_residues	360
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	76.7 Å
Rg (real space) rg_real	23.97 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	2.9370e+07
I(0) uncertainty (real space) i0_real_error	3.7010e+05
Rg (reciprocal space) rg_reciprocal	23.98 Å
I(0) (reciprocal space) i0_reciprocal	29370000.0000
Solution quality estimate total_estimate	0.9043
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.307
Kurtosis Kurtosis kurtosis	-0.446
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5647000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Retinoblastoma-like protein 1,Retinoblastoma-like protein 1
Molecular weight formula_weight	43037.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3082

GEFTQSVSRLQSIVAGLKNAPSDQLINIFESCVRNPVENIMKILKGIGETFCQHYTQSTDEQPGSHIDFAVNRLKLAEILYYKILETVMVQETRRLHGMDMSVLLEQDIFHRSLMACCLEIVLFAYSSPRTFPWIIEVLNLQPFYFYKVIEVVIRSEEGLSRDMVKHLNSIEEQILESLAWSHDSALWEALQVSANKVPTCEEVIFPNNFETGRPKRTGSLALFYRKVYHLASVRLRDLCLKLDVSNELRRKIWTCFEFTLVHCPDLMKDRHLDQLLLCAFYIMAKVTKEERTFQEIMKSYRNQPQANSHVYRSVLLKSIKEERGDLIKFYNTIYVGRVKSFALKYDLANQDHMMDAPPLSPFPHIKQQ

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	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 polymer

Description description	LIN52 peptide
Molecular weight formula_weight	2359.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

EASLLSFEKLDRASADLWPE

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4yooA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	4yooA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

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8. Citations (1)

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Unit-cell length a length_a	74.815 Å
Unit-cell length b length_b	100.530 Å
Unit-cell length c length_c	142.790 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	71.395 Å
R factor r_factor	0.2002
R_work r_work	0.1954
R_free r_free	0.2421

fit	/app/data/saxs_computation/yo/4yoo/4yoo.fit
pddf	/app/data/pr_computation/yo/4yoo/4yoo.pr.out
profile	/app/data/saxs_computation/yo/4yoo/4yoo.dat

p107 pocket domain in complex with LIN52 P29A peptide

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

Retinoblastoma-like protein 1,Retinoblastoma-like 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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)