SAXSdb — 3ktv

▼

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

Signal recognition particle 19 kDa protein

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–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain B； UniProt 1–120	Not recorded	SRP RNA × 1 K POTASSIUM ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；100 mM NaOAc, 0.75 M KF, 2.2 M (NH4)2SO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.80 Å R-free 0.329
2	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain D； UniProt 1–120	Not recorded	SRP RNA × 1 K POTASSIUM ION × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；100 mM NaOAc, 0.75 M KF, 2.2 M (NH4)2SO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.80 Å R-free 0.329

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 3KTV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JID Human SRP19 in complex with helix 6 of Human SRP RNA Deposited 2001-07-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–120（120 aa） Fragment：24 C-TERMINAL RESIDUES TRUNCATED	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；potassium chloride, magnesium chloride, sodium chloride, PEG 3350, isopropanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.222
1MFQ Crystal Structure Analysis of a Ternary S-Domain Complex of Human Signal Recognition Particle Deposited 2002-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain B 14–120（107 aa）	Not recorded	MG MAGNESIUM ION × 5 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300.5 K；14% (w/v) PEG8000, 100mM Na-cacodylate, 400mM lithium sulfate, 80mM magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300.5K	Resolution 3.10 Å R-free 0.267
2J37 MODEL OF MAMMALIAN SRP BOUND TO 80S RNCS Deposited 2006-08-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric	Chain B 14–120（107 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.70 Å
4P3E Structure of the human SRP S domain Deposited 2014-03-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain B 1–120（120 aa） Fragment：UNP residues 1-120	Not recorded	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.2；291 K；Ammonium sulfate, Sodium malonate	Resolution 3.50 Å R-free 0.285
5M73 Structure of the human SRP S domain with SRP72 RNA-binding domain Deposited 2016-10-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain B 11–118（108 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain F 11–118（108 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
7NFX Mammalian ribosome nascent chain complex with SRP and SRP receptor in early state A Deposited 2021-02-08	Different construct 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 q 1–144（144 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
7QWQ Ternary complex of ribosome nascent chain with SRP and NAC Deposited 2022-01-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 52-meric	Chain q 1–144（144 aa）	Not recorded	MG MAGNESIUM ION × 97 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.83 Å

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SRP19_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–120； UniProt 1–120 Author chain D； PDBConstruct 1–120； UniProt 1–120

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3ktv
Deposition date deposition_date	2009-11-26
Structure title title	Crystal structure of the human SRP19/S-domain SRP RNA complex
Keywords keywords	;ribonucleoprotein complex, RNA-RNA tertiary interactions, asymmetric loop, RNA-binding, Signal recognition particle, RNA-RNA Binding Protein complex ;; RNA/RNA Binding Protein
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	34.76 Å
Radius of gyration Rg (electron density) rg_electron	33.46 Å
Forward intensity I(0) i0	337584000.00
Molecular weight molecular_weight	95390.0 kDa
Excluded volume excluded_volume	96737 Å³
Envelope volume envelope_volume	151260 Å³
Hydration-shell volume shell_volume	39277 Å³
Envelope diameter envelope_diameter	126.8 Å
Shell Rg shell_rg	38.47 Å
Envelope Rg envelope_rg	33.08 Å
Shape Rg shape_rg	33.35 Å
Total Rg total_rg	33.89 Å
Total atoms total_atoms	6390
Residues n_residues	429
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

▼

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

Maximum dimension Dmax dmax	119.2 Å
Rg (real space) rg_real	34.86 Å
Rg uncertainty (real space) rg_real_error	1.33 Å
I(0) (real space) i0_real	3.3760e+08
I(0) uncertainty (real space) i0_real_error	5.8570e+06
Rg (reciprocal space) rg_reciprocal	34.80 Å
I(0) (reciprocal space) i0_reciprocal	337600000.0000
Solution quality estimate total_estimate	0.8747
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.9 Å
Skewness Skewness skewness	0.410
Kurtosis Kurtosis kurtosis	-0.190
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12960000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.829

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	SRP RNA
Molecular weight formula_weight	35091.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	6390

GCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGUA

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 polymer

Description description	Signal recognition particle 19 kDa protein
Molecular weight formula_weight	14791.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MACAAARSPADQDRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTRTQLEHHHHHH

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 3 Entity 3 polymer

Description description	SRP RNA
Molecular weight formula_weight	35170.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C

GCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGUA

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 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3ktvB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily	30 — Signal recognition particle, SRP19-like subunit

Domain ID domain_id	3ktvD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	56 — Phenylalanyl-tRNA Synthetase; Chain B, domain 1
Homologous superfamily homologous superfamily	30 — Signal recognition particle, SRP19-like subunit

▶

8. Citations (1)

▶

Unit-cell length a length_a	100.120 Å
Unit-cell length b length_b	100.120 Å
Unit-cell length c length_c	293.300 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	3.800 Å
Low-resolution limit resolution_low	70.010 Å
R factor r_factor	0.2930
R_work r_work	0.2910
R_free r_free	0.3290

fit	/app/data/saxs_computation/kt/3ktv/3ktv.fit
pddf	/app/data/pr_computation/kt/3ktv/3ktv.pr.out
profile	/app/data/saxs_computation/kt/3ktv/3ktv.dat

Crystal structure of the human SRP19/S-domain SRP RNA complex

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

Signal recognition particle 19 kDa protein

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)