SAXSdb — 5wrw

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

Signal recognition particle subunit SRP72

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–163 Chain B； UniProt 1–163	Fragment：UNP residues 1-163	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；(NH4)2SO4	Resolution 2.91 Å R-free 0.266
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–163 Chain D； UniProt 1–163	Fragment：UNP residues 1-163	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；(NH4)2SO4	Resolution 2.91 Å R-free 0.266
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 1–163 Chain F； UniProt 1–163	Fragment：UNP residues 1-163	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；(NH4)2SO4	Resolution 2.91 Å R-free 0.266

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 5WRW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5M72 Structure of the human SRP68-72 protein-binding domain complex Deposited 2016-10-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 10–166（157 aa）	Not recorded	SO4 SULFATE ION × 2 K POTASSIUM ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M K2SO4 20% (w/v) PEG 3350	Resolution 1.60 Å R-free 0.184
5M73 Structure of the human SRP S domain with SRP72 RNA-binding domain Deposited 2016-10-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain D 512–668（157 aa）	Not recorded	MG MAGNESIUM ION × 30 K POTASSIUM ION × 5 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；17 % (w/v) PEG3350 0.1 M KF 0.1 M Tris pH 8.5	Resolution 3.40 Å R-free 0.280
5M73 Structure of the human SRP S domain with SRP72 RNA-binding domain Deposited 2016-10-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain H 512–668（157 aa）	Not recorded	MG MAGNESIUM ION × 15 K POTASSIUM ION × 5 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；17 % (w/v) PEG3350 0.1 M KF 0.1 M Tris pH 8.5	Resolution 3.40 Å R-free 0.280
5WRV Complex structure of human SRP72/SRP68 Deposited 2016-12-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–163（163 aa） Fragment：UNP residues 1-163	Not recorded	ACT ACETATE ION × 2 GOL GLYCEROL × 5 SO4 SULFATE ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；(NH4)2SO4	Resolution 1.70 Å R-free 0.189
7NFX Mammalian ribosome nascent chain complex with SRP and SRP receptor in early state A Deposited 2021-02-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 55-meric	Chain z 1–671（671 aa）	Not recorded	ZN ZINC ION × 5 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.20 Å
8QVW Cryo-EM structure of the peptide binding domain of human SRP68/72 Deposited 2023-10-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–671（671 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8QVX Structure of the PBD of human SRP68/72 (cryoSPARC 3DFlex) Deposited 2023-10-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–671（671 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SRP72_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–163； UniProt 1–163 Author chain B； PDBConstruct 1–163； UniProt 1–163 Author chain C； PDBConstruct 1–163； UniProt 1–163 Author chain D； PDBConstruct 1–163； UniProt 1–163 Author chain E； PDBConstruct 1–163； UniProt 1–163 Author chain F； PDBConstruct 1–163； UniProt 1–163

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	5wrw
Deposition date deposition_date	2016-12-04
Structure title title	Structure of human apo-SRP72
Keywords keywords	Complex, human, SRP72, SRP68, signal recognition particle, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	50.29 Å
Radius of gyration Rg (electron density) rg_electron	50.45 Å
Forward intensity I(0) i0	117184000.00
Molecular weight molecular_weight	87441.0 kDa
Excluded volume excluded_volume	108990 Å³
Envelope volume envelope_volume	199020 Å³
Hydration-shell volume shell_volume	34580 Å³
Envelope diameter envelope_diameter	159.2 Å
Shell Rg shell_rg	51.50 Å
Envelope Rg envelope_rg	47.71 Å
Shape Rg shape_rg	50.43 Å
Total Rg total_rg	50.56 Å
Total atoms total_atoms	6153
Residues n_residues	780
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	147.0 Å
Rg (real space) rg_real	50.44 Å
Rg uncertainty (real space) rg_real_error	1.64 Å
I(0) (real space) i0_real	1.1720e+08
I(0) uncertainty (real space) i0_real_error	2.3060e+06
Rg (reciprocal space) rg_reciprocal	50.13 Å
I(0) (reciprocal space) i0_reciprocal	117100000.0000
Solution quality estimate total_estimate	0.5153
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	52.1 Å
Skewness Skewness skewness	0.178
Kurtosis Kurtosis kurtosis	-0.899
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2837000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.616; Stabil: 0.977; Sysdev: 0.029; Positv: 1.000; Valcen: 0.822; Smooth: 0.008

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Signal recognition particle subunit SRP72
Molecular weight formula_weight	18478.7 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	6248

MASGGSGGVSVPALWSEVNRYGQNGDFTRALKTVNKILQINKDDVTALHCKVVCLIQNGSFKEALNVINTHTKVLANNSLSFEKAYCEYRLNRIENALKTIESANQQTDKLKELYGQVLYRLERYDECLAVYRDLVRNSQDDYDEERKTNLSAVVAAQSNWEK

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

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

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8. Citations (1)

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Unit-cell length a length_a	83.435 Å
Unit-cell length b length_b	123.715 Å
Unit-cell length c length_c	150.723 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.910 Å
Low-resolution limit resolution_low	50.010 Å
R factor r_factor	0.2337
R_work r_work	0.2319
R_free r_free	0.2664

fit	/app/data/saxs_computation/wr/5wrw/5wrw.fit
pddf	/app/data/pr_computation/wr/5wrw/5wrw.pr.out
profile	/app/data/saxs_computation/wr/5wrw/5wrw.dat

Structure of human apo-SRP72

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

Signal recognition particle subunit SRP72

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