SAXSdb — 4p3e

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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 Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain B； UniProt 1–120	Fragment：UNP residues 1-120	SRP RNA (124-mer) × 1 Signal recognition particle subunit SRP68 × 1 （Q9UHB9） 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

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 4P3E	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 oligomeric state 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 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
3KTV Crystal structure of the human SRP19/S-domain SRP RNA complex Deposited 2009-11-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–120（120 aa）	Not recorded	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
3KTV Crystal structure of the human SRP19/S-domain SRP RNA complex Deposited 2009-11-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain D 1–120（120 aa）	Not recorded	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
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 9 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

Signal recognition particle subunit SRP68

Homo sapiens

UniProt Q9UHB9

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 Heteromer Protein × 2 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain C； UniProt 47–254	Fragment：UNP residues 47-254 Mutation：E108D	SRP RNA (124-mer) × 1 Signal recognition particle 19 kDa protein × 1 （P09132） 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

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 4P3E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4P3F Structure of the human SRP68-RBD Deposited 2014-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 47–254（208 aa） Fragment：UNP residues 47-254 Chain B 47–254（208 aa） Fragment：UNP residues 47-254	Mutation：E108D Mutation：E108D	PEG DI(HYDROXYETHYL)ETHER × 3 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；K/Na tartrate, PEG5000MME	Resolution 1.70 Å R-free 0.219
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 B 546–614（69 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 C 60–254（195 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 G 60–254（195 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 A 509–614（106 aa） Fragment：UNP residues 509-614	Mutation：E608A, Q609A, K610A	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 u 1–627（627 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 mutation/modification 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 v 1–627（627 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
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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 52–627（576 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 52–627（576 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

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

View Construct and Data Evidence

UniProt name	SRP68_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 9–216； UniProt 47–254

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	4p3e
Deposition date deposition_date	2014-03-07
Structure title title	Structure of the human SRP S domain
Keywords keywords	SRP, SRP RNA, SRP19, SRP68, ribonucleoprotein particle (RNP), Arginine-rich motif (ARM), RNA BINDING PROTEIN-RNA complex; RNA BINDING PROTEIN/RNA
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	33.98 Å
Radius of gyration Rg (electron density) rg_electron	35.78 Å
Forward intensity I(0) i0	167410000.00
Molecular weight molecular_weight	73807.0 kDa
Excluded volume excluded_volume	79296 Å³
Envelope volume envelope_volume	118420 Å³
Hydration-shell volume shell_volume	30077 Å³
Envelope diameter envelope_diameter	125.1 Å
Shell Rg shell_rg	38.41 Å
Envelope Rg envelope_rg	35.59 Å
Shape Rg shape_rg	35.83 Å
Total Rg total_rg	35.81 Å
Total atoms total_atoms	5011
Residues n_residues	408
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	117.1 Å
Rg (real space) rg_real	34.35 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	1.6740e+08
I(0) uncertainty (real space) i0_real_error	2.7250e+06
Rg (reciprocal space) rg_reciprocal	34.12 Å
I(0) (reciprocal space) i0_reciprocal	167400000.0000
Solution quality estimate total_estimate	0.6083
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.9 Å
Skewness Skewness skewness	0.573
Kurtosis Kurtosis kurtosis	-0.391
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9746000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.663; Stabil: 1.000; Sysdev: 0.214; Positv: 1.000; Valcen: 0.486; Smooth: 0.786

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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	SRP RNA (124-mer)
Molecular weight formula_weight	40549.2 kDa
Mutation mutation	C114G, G237U, G238A
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	5140

GACUAAGUUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGAUCAGUAGUUA

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

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	Signal recognition particle subunit SRP68
Molecular weight formula_weight	25604.2 kDa
Mutation mutation	E108D
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGHHHHHHGSKANKEFGDSLSLEILQIIKESQQQHGLRHGDFQRYRGYCSRRQRRLRKTLNFKMGNRHKFTGKKVTEDLLTDNRYLLLVLMDAERAWSYAMQLKQEANTEPRKRFHLLSRLRKAVKHAEELERLCESNRVDAKTKLEAQAYTAYLSGMLRFEHQEWKAAIEAFNKCKTIYEKLASAFTEEQAVLYNQRVEEISPNIRYCAYNIGDQ

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	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4p3eB00
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	4p3eC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3450 — Hyaluronidase domain-like
Homologous superfamily homologous superfamily	40 — Signal recognition particle, SRP68 subunit, RNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	125.649 Å
Unit-cell length b length_b	70.530 Å
Unit-cell length c length_c	106.493 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.46 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	44.089 Å
R factor r_factor	0.2456
R_work r_work	0.2437
R_free r_free	0.2851

fit	/app/data/saxs_computation/p3/4p3e/4p3e.fit
pddf	/app/data/pr_computation/p3/4p3e/4p3e.pr.out
profile	/app/data/saxs_computation/p3/4p3e/4p3e.dat

Structure of the human SRP S domain

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

Signal recognition particle subunit SRP68

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

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

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)