SAXSdb — 5mfy

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

RNA-binding protein 5

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 451–511	Fragment：UNP residues 451-511	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 70；Pressure 1 NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 70；Pressure 1 NMR sample composition：1 mM [U-100% 13C; U-100% 15N] ocre5, 20 mM sodium phosphate, 50 mM sodium chloride, 10 % D2O, 90 % H2O, 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 5MFY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LK0 Solution structure and binding studies of the RanBP2-type zinc finger of RBM5 Deposited 2011-09-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 181–210（30 aa） Fragment：RanBP2-type zinc finger residues 181-210	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 5.7；293 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 100 uM RBM5-ZF1, 150 uM ZINC ION, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LK1 Solution structure and binding studies of the RanBP2-type zinc finger of RBM5 Deposited 2011-09-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 181–210（30 aa） Fragment：RanBP2-type zinc finger residues 181-210	Non-standard monomer：Yes (specific site not provided by mmCIF)	AQN 9,10-dioxo-9,10-dihydroanthracene-2-sulfonic acid × 1 ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 5.7；293 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 100 uM RBM5-ZF1, 150 uM ZINC ION, 500 uM AQN, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LKZ Solution structure of the second RRM domain of RBM5 Deposited 2011-10-23	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 231–316（86 aa） Fragment：RRM 2 domain, UNP residues 231-316	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；298 K；Pressure ambient NMR sample composition 40 mM sodium phosphate-1, 50 mM sodium chloride-2, 2 mM EDTA-3, 1 mM sodium azide-4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 40 mM sodium phosphate-5, 50 mM sodium chloride-6, 2 mM EDTA-7, 1 mM sodium azide-8, 100% D2O \| 100% D2O	Resolution not provided
5MF9 Solution structure of the RBM5 OCRE domain in complex with polyproline SmN peptide. Deposited 2016-11-17	Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 451–511（61 aa） Fragment：UNP residues 451-511	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 2 mM [U-99% 15N] 15N, 2 mM [U-99% 13C; U-99% 15N] 13C_15N, 2 mM [U-13C; U-15N] unlabel, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
7PCV Crystal structure of RBM5 RRM1-zinc finger Deposited 2021-08-04	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 94–210（117 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M BICINE pH 8.5, 12% PEG 6000, 10% 1M cesium chloride	Resolution 2.42 Å R-free 0.313
7PCV Crystal structure of RBM5 RRM1-zinc finger Deposited 2021-08-04	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 94–210（117 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M BICINE pH 8.5, 12% PEG 6000, 10% 1M cesium chloride	Resolution 2.42 Å R-free 0.313
9ZE0 Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (Proximal DHX15 state) Deposited 2025-11-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain A 1–815（815 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；20 mM HEPES-KOH pH 7.9, 150 mM NaCl, 1.5 mM MgCl2, 10 mM DTT, 4.5% glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å
9ZE2 Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (core) Deposited 2025-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain A 1–815（815 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；20 mM HEPES-KOH pH 7.9, 150 mM NaCl, 1.5 mM MgCl2, 10 mM DTT, 4.5% glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.26 Å
9ZE3 Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (Distal DHX15 state) Deposited 2025-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain A 1–815（815 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；20 mM HEPES-KOH pH 7.9, 150 mM NaCl, 1.5 mM MgCl2, 10 mM DTT, 4.5% glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.93 Å
9ZEC Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (SF3A state 1) Deposited 2025-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: tridecameric	Chain A 1–815（815 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；20 mM HEPES-KOH pH 7.9, 150 mM NaCl, 1.5 mM MgCl2, 10 mM DTT, 4.5% glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.61 Å
9ZED Cryo-EM structure of the endogenous U2/branchpoint spliceosomal complex (SF3A state 2) Deposited 2025-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: tridecameric	Chain A 1–815（815 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；20 mM HEPES-KOH pH 7.9, 150 mM NaCl, 1.5 mM MgCl2, 10 mM DTT, 4.5% glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.94 Å

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RBM5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–64； UniProt 451–511

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	5mfy
Deposition date deposition_date	2016-11-19
Structure title title	RBM5 OCRE domain
Keywords keywords	splicing, ocre; SPLICING
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	12.60 Å
Radius of gyration Rg (electron density) rg_electron	12.14 Å
Forward intensity I(0) i0	82245300.00
Molecular weight molecular_weight	74278.0 kDa
Excluded volume excluded_volume	91643 Å³
Envelope volume envelope_volume	16759 Å³
Hydration-shell volume shell_volume	10464 Å³
Envelope diameter envelope_diameter	50.2 Å
Shell Rg shell_rg	19.39 Å
Envelope Rg envelope_rg	15.19 Å
Shape Rg shape_rg	12.01 Å
Total Rg total_rg	12.88 Å
Total atoms total_atoms	9820
Residues n_residues	640
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	46.9 Å
Rg (real space) rg_real	12.65 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	8.2250e+07
I(0) uncertainty (real space) i0_real_error	9.2430e+05
Rg (reciprocal space) rg_reciprocal	12.64 Å
I(0) (reciprocal space) i0_reciprocal	82250000.0000
Solution quality estimate total_estimate	0.8038
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.4 Å
Skewness Skewness skewness	0.458
Kurtosis Kurtosis kurtosis	0.133
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	85500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.521; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.884; Smooth: 0.998

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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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Description description	RNA-binding protein 5
Molecular weight formula_weight	7436.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9820

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

fit	/app/data/saxs_computation/mf/5mfy/5mfy.fit
pddf	/app/data/pr_computation/mf/5mfy/5mfy.pr.out
profile	/app/data/saxs_computation/mf/5mfy/5mfy.dat

RBM5 OCRE domain

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

RNA-binding protein 5

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)