SAXSdb — 2mjf

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

Ribosome assembly 1 protein

Saccharomyces cerevisiae

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 317–352	Not recorded	Protein HIT1 × 1 （P46973）	SOLUTION NMR NMR measurement conditions：pH 6.4；293 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR sample composition：1 mM [U-100% 13C; U-100% 15N] rsa, 1 mM [U-100% 13C; U-100% 15N] hit, 150 mM sodium chloride, 90 % H2O, 10 % [U-100% 2H] D2O, 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 2MJF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2M3F NMR structure of Rsa1p238-259 from S. Cerevisiae Deposited 2013-01-17	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 238–259（22 aa） Fragment：UNP residues 238-259	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.7；293 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR measurement conditions pH 3.7；305 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR sample composition 2 mM protein, 10 mM potassium phosphate, 150 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
4NUT Crystal structure of the complex between Snu13p and the PEP domain of Rsa1 Deposited 2013-12-04	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 238–290（53 aa） Fragment：PEP domain, UNP residues 238-290	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；2.3M ammonium sulfate, 70mM sodium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.55 Å R-free 0.235

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RSA1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–40； UniProt 317–352

Protein HIT1

Saccharomyces cerevisiae

UniProt P46973

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 B； UniProt 70–164	Not recorded	Ribosome assembly 1 protein × 1 （Q08932）	SOLUTION NMR NMR measurement conditions：pH 6.4；293 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR sample composition：1 mM [U-100% 13C; U-100% 15N] rsa, 1 mM [U-100% 13C; U-100% 15N] hit, 150 mM sodium chloride, 90 % H2O, 10 % [U-100% 2H] D2O, 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 2MJF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2N95 NMR structure of yeast Hit1 protein zinc finger Deposited 2015-11-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–46（46 aa） Fragment：zinc finger domain (UNP residues 1-46)	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 160；Pressure ambient NMR measurement conditions pH 6.4；313 K；Ionic strength (raw mmCIF value) 160；Pressure ambient NMR sample composition 2.2 mM [U-100% 13C; U-100% 15N] protein, 10 mM sodium phosphate, 150 mM sodium chloride, 0.5 mM TCEP, 3 mM [U-2H] DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HIT1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–95； UniProt 70–164

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	2mjf
Deposition date deposition_date	2014-01-08
Structure title title	Solution structure of the complex between the yeast Rsa1 and Hit1 proteins
Keywords keywords	PROTEIN BINDING; PROTEIN BINDING
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	15.56 Å
Radius of gyration Rg (electron density) rg_electron	14.95 Å
Forward intensity I(0) i0	1287400000.00
Molecular weight molecular_weight	308830.0 kDa
Excluded volume excluded_volume	388100 Å³
Envelope volume envelope_volume	37614 Å³
Hydration-shell volume shell_volume	17802 Å³
Envelope diameter envelope_diameter	58.2 Å
Shell Rg shell_rg	23.83 Å
Envelope Rg envelope_rg	18.11 Å
Shape Rg shape_rg	14.91 Å
Total Rg total_rg	15.26 Å
Total atoms total_atoms	43480
Residues n_residues	2700
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	50.2 Å
Rg (real space) rg_real	15.47 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	1.2870e+09
I(0) uncertainty (real space) i0_real_error	1.4410e+07
Rg (reciprocal space) rg_reciprocal	15.48 Å
I(0) (reciprocal space) i0_reciprocal	1287000000.0000
Solution quality estimate total_estimate	0.8874
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.0 Å
Skewness Skewness skewness	0.110
Kurtosis Kurtosis kurtosis	-0.385
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	381600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.991

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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	Ribosome assembly 1 protein
Molecular weight formula_weight	4543.0 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	43480

GPHMFANENSQLLDFIRELGDVGLLEYELSQQEKDVLFGS

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protein HIT1
Molecular weight formula_weight	10920.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MNKTLKTKAFDDIYQNSAELQELLKYNTVKFHLAKVYRILSSTVNDGSSGKMNSDLQKELAVNYLNTLRYGGIHYNEAIEEFCQILLDKLNAVKK

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	yeast
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2mjfA00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	1790 —

Domain ID domain_id	2mjfB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	260 —

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8. Citations (1)

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fit	/app/data/saxs_computation/mj/2mjf/2mjf.fit
pddf	/app/data/pr_computation/mj/2mjf/2mjf.pr.out
profile	/app/data/saxs_computation/mj/2mjf/2mjf.dat

Solution structure of the complex between the yeast Rsa1 and Hit1 proteins

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

Ribosome assembly 1 protein

State in the Current Structure

Other States of the Same Protein in the Database

Protein HIT1

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)