SAXSdb — 3kl4

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

Signal recognition 54 kDa protein

Sulfolobus solfataricus

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 2–432	Fragment：UNP residues 2-432	Signal peptide of yeast dipeptidyl aminopeptidase B × 1 （P18962）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.5；295 K；5-7 % PEG 4000, 100 mM Bis-Tris, 100 mM NaCl, 5-50 mM Mg(OAc)2, 2 % Polypropylene glycol P400. Crystals were obtained by seeding, pH 5.5, VAPOR DIFFUSION, temperature 295K	Resolution 3.50 Å R-free 0.322

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 3KL4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QZW Crystal structure of the complete core of archaeal SRP and implications for inter-domain communication Deposited 2003-09-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–432（432 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Ammonium sulphate, sodium chloride, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 4.10 Å R-free 0.387
1QZW Crystal structure of the complete core of archaeal SRP and implications for inter-domain communication Deposited 2003-09-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain C 1–432（432 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Ammonium sulphate, sodium chloride, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 4.10 Å R-free 0.387
1QZW Crystal structure of the complete core of archaeal SRP and implications for inter-domain communication Deposited 2003-09-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain E 1–432（432 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Ammonium sulphate, sodium chloride, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 4.10 Å R-free 0.387
1QZW Crystal structure of the complete core of archaeal SRP and implications for inter-domain communication Deposited 2003-09-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain G 1–432（432 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；Ammonium sulphate, sodium chloride, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 4.10 Å R-free 0.387
1QZX Crystal structure of the complete core of archaeal SRP and implications for inter-domain communication Deposited 2003-09-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–432（432 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG 8000, litium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 4.00 Å R-free 0.383
1QZX Crystal structure of the complete core of archaeal SRP and implications for inter-domain communication Deposited 2003-09-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–432（432 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG 8000, litium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 4.00 Å R-free 0.383
3ZN8 Structural Basis of Signal Sequence Surveillance and Selection by the SRP-SR Complex Deposited 2013-02-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric	Chain M 307–431（125 aa） Fragment：M, RESIDUES 327-431	Not recorded	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 50 MM HEPES-KOH, 100 MM KOAC, 8 MM MG(OAC)2, PH 7.5；pH 7.5；50 MM HEPES-KOH, 100 MM KOAC, 8 MM MG(OAC)2, PH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN；THE GRIDS WERE PLUNGE FROZEN IN LIQUID ETHANE USING A FEI MARK IV VITRIFICATION ROBOT AFTER BLOTTING FOR 1 S AT RT AND 100 PER CENT RELATIVE HUMIDITY	Resolution 12.00 Å
5L3S Structure of the GTPase heterodimer of crenarchaeal SRP54 and FtsY Deposited 2016-05-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–292（292 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 5GP GUANOSINE-5'-MONOPHOSPHATE × 1 GOL GLYCEROL × 7 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES pH 5.8, 1.26 M ammonium sulfate	Resolution 1.90 Å R-free 0.216
5L3S Structure of the GTPase heterodimer of crenarchaeal SRP54 and FtsY Deposited 2016-05-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–292（292 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 5GP GUANOSINE-5'-MONOPHOSPHATE × 1 GOL GLYCEROL × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES pH 5.8, 1.26 M ammonium sulfate	Resolution 1.90 Å R-free 0.216
5L3S Structure of the GTPase heterodimer of crenarchaeal SRP54 and FtsY Deposited 2016-05-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–292（292 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 5GP GUANOSINE-5'-MONOPHOSPHATE × 1 GOL GLYCEROL × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES pH 5.8, 1.26 M ammonium sulfate	Resolution 1.90 Å R-free 0.216
5L3S Structure of the GTPase heterodimer of crenarchaeal SRP54 and FtsY Deposited 2016-05-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–292（292 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 5GP GUANOSINE-5'-MONOPHOSPHATE × 1 GOL GLYCEROL × 5 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM MES pH 5.8, 1.26 M ammonium sulfate	Resolution 1.90 Å R-free 0.216
5L3V Structure of the crenarchaeal SRP54 GTPase bound to GDP Deposited 2016-05-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–293（293 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M CHES pH 6.0, 15 % (w/v) PEG 8000, 0.2 M ammonium sulfate	Resolution 2.30 Å R-free 0.222
5L3V Structure of the crenarchaeal SRP54 GTPase bound to GDP Deposited 2016-05-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–293（293 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M CHES pH 6.0, 15 % (w/v) PEG 8000, 0.2 M ammonium sulfate	Resolution 2.30 Å R-free 0.222

5 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SRP54_SULSO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–433； UniProt 2–432

Signal peptide of yeast dipeptidyl aminopeptidase B

Saccharomyces cerevisiae

UniProt P18962

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 26–51	Fragment：UNP residues 26-51	Signal recognition 54 kDa protein × 1 （Q97ZE7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.5；295 K；5-7 % PEG 4000, 100 mM Bis-Tris, 100 mM NaCl, 5-50 mM Mg(OAc)2, 2 % Polypropylene glycol P400. Crystals were obtained by seeding, pH 5.5, VAPOR DIFFUSION, temperature 295K	Resolution 3.50 Å R-free 0.322

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 3KL4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ZN8 Structural Basis of Signal Sequence Surveillance and Selection by the SRP-SR Complex Deposited 2013-02-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric	Chain S 31–44（14 aa） Fragment：RESIDUES 31-44	Not recorded	MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 50 MM HEPES-KOH, 100 MM KOAC, 8 MM MG(OAC)2, PH 7.5；pH 7.5；50 MM HEPES-KOH, 100 MM KOAC, 8 MM MG(OAC)2, PH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN；THE GRIDS WERE PLUNGE FROZEN IN LIQUID ETHANE USING A FEI MARK IV VITRIFICATION ROBOT AFTER BLOTTING FOR 1 S AT RT AND 100 PER CENT RELATIVE HUMIDITY	Resolution 12.00 Å
7OBR RNC-SRP early complex Deposited 2021-04-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric	Chain s 24–90（67 aa）	Not recorded	MG MAGNESIUM ION × 97 ZN ZINC ION × 5 GDP GUANOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.80 Å

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

View Construct and Data Evidence

UniProt name	DAP2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 12–37； UniProt 26–51

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	3kl4
Deposition date deposition_date	2009-11-06
Structure title title	Recognition of a signal peptide by the signal recognition particle
Keywords keywords	;signal recognition particle, SRP, SRP54, Ffh, signal sequence, signal peptide, GTP-binding, Nucleotide-binding, Ribonucleoprotein, RNA-binding, Signal-anchor, Transmembrane, HYDROLASE ;; HYDROLASE
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	30.08 Å
Radius of gyration Rg (electron density) rg_electron	29.30 Å
Forward intensity I(0) i0	34591700.00
Molecular weight molecular_weight	48109.0 kDa
Excluded volume excluded_volume	61459 Å³
Envelope volume envelope_volume	85096 Å³
Hydration-shell volume shell_volume	24992 Å³
Envelope diameter envelope_diameter	95.3 Å
Shell Rg shell_rg	35.47 Å
Envelope Rg envelope_rg	28.76 Å
Shape Rg shape_rg	29.27 Å
Total Rg total_rg	30.11 Å
Total atoms total_atoms	3385
Residues n_residues	434
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	94.7 Å
Rg (real space) rg_real	30.13 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	3.4590e+07
I(0) uncertainty (real space) i0_real_error	5.7340e+05
Rg (reciprocal space) rg_reciprocal	30.12 Å
I(0) (reciprocal space) i0_reciprocal	34590000.0000
Solution quality estimate total_estimate	0.8700
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.2 Å
Skewness Skewness skewness	0.216
Kurtosis Kurtosis kurtosis	-0.859
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14660000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.860; Smooth: 0.936

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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	Signal recognition 54 kDa protein
Molecular weight formula_weight	48503.4 kDa
EC 编号 ec_number	3.6.5.4
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	3385

MGLENIRDAVRKFLTGSTPYEKAVDEFIKDLQKSLISSDVNVKLVFSLTAKIKERLNKEKPPSVLERKEWFISIVYDELSKLFGGDKEPNVNPTKLPFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAADVYRPAAYDQLLQLGNQIGVQVYGEPNNQNPIEIAKKGVDIFVKNKMDIIIVDTAGRHGYGEETKLLEEMKEMYDVLKPDDVILVIDASIGQKAYDLASRFHQASPIGSVIITKMDGTAKGGGALSAVVATGATIKFIGTGEKIDELETFNAKRFVSRILGMGDIESILEKVKGLEEYDKIQKKMEDVMEGKGKLTLRDVYAQIIALRKMGPLSKVLQHIPGLGIMLPTPSEDQLKIGEEKIRRWLAALNSMTYKELENPNIIDKSRMRRIAEGSGLEVEEVRELLEWYNNMNRLLKMVK

来源 Source

来源生物 organism	Sulfolobus solfataricus
NCBI Class编号 ncbi_taxonomy_id	273057
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Signal peptide of yeast dipeptidyl aminopeptidase B
Molecular weight formula_weight	4533.4 kDa
EC 编号 ec_number	3.4.14.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ARSGSGSGSGSKLIRVGIILVLLIWGTVLLLKSIPHHHHHHH

来源 Source

来源生物 organism	Saccharomyces cerevisiae
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3kl4A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	140 — SRP54, nucleotide-binding domain

Domain ID domain_id	3kl4A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3kl4A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	30 — Signal recognition particle, SRP54 subunit, M-domain

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8. Citations (6)

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Unit-cell length a length_a	91.883 Å
Unit-cell length b length_b	91.883 Å
Unit-cell length c length_c	133.263 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	58.420 Å
R factor r_factor	0.3010
R_work r_work	0.3010
R_free r_free	0.3220

fit	/app/data/saxs_computation/kl/3kl4/3kl4.fit
pddf	/app/data/pr_computation/kl/3kl4/3kl4.pr.out
profile	/app/data/saxs_computation/kl/3kl4/3kl4.dat

Recognition of a signal peptide by the signal recognition particle

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

Signal recognition 54 kDa protein

State in the Current Structure

Other States of the Same Protein in the Database

Signal peptide of yeast dipeptidyl aminopeptidase B

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

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) 3 domains

CATH v4.4 (3 domains)

8. Citations (6)

9. Files and Curves (10)

Files (7)

Curves (3)