SAXSdb — 1mfq

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

signal recognition particle 19kDa 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 14–120	Not recorded	7S RNA of human SRP × 1 signal recognition particle 54kDa protein × 1 （P61011） 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

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 1MFQ	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
2J37 MODEL OF MAMMALIAN SRP BOUND TO 80S RNCS Deposited 2006-08-18	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
4P3E Structure of the human SRP S domain Deposited 2014-03-07	Different construct 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 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 2–108； UniProt 14–120

signal recognition particle 54kDa protein

Homo sapiens

UniProt P61011

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 323–441	Fragment：M-domain	7S RNA of human SRP × 1 signal recognition particle 19kDa protein × 1 （P09132） 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

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 1MFQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QB2 CRYSTAL STRUCTURE OF THE CONSERVED SUBDOMAIN OF HUMAN PROTEIN SRP54M AT 2.1A RESOLUTION: EVIDENCE FOR THE MECHANISM OF SIGNAL PEPTIDE BINDING Deposited 1999-04-29	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 326–434（109 aa） Fragment：SRP54 Chain B 326–434（109 aa） Fragment：SRP54	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；30% PEG 2K, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.318
5L3Q Structure of the GTPase heterodimer of human SRP54 and SRalpha Deposited 2016-05-24	Different construct 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 1–436（436 aa）	Not recorded	SO4 SULFATE ION × 5 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 GOL GLYCEROL × 2 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100 mM Tris pH 8.0, 400 mM lithium sulfate, 10 % (w/v) PEG 8000	Resolution 3.20 Å R-free 0.191
5L3Q Structure of the GTPase heterodimer of human SRP54 and SRalpha Deposited 2016-05-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–436（436 aa）	Not recorded	SO4 SULFATE ION × 4 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 GOL GLYCEROL × 2 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；100 mM Tris pH 8.0, 400 mM lithium sulfate, 10 % (w/v) PEG 8000	Resolution 3.20 Å R-free 0.191
6Y2Z NG domain of human SRP54 Deposited 2020-02-17	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 1–296（296 aa）	Not recorded	PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；na2hpo4 0.8 M K2HPO4 0.8 M HEPES 0.1 M (pH 7.5)	Resolution 2.15 Å R-free 0.246
6Y2Z NG domain of human SRP54 Deposited 2020-02-17	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 1–296（296 aa）	Not recorded	PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；na2hpo4 0.8 M K2HPO4 0.8 M HEPES 0.1 M (pH 7.5)	Resolution 2.15 Å R-free 0.246
6Y30 NG domain of human SRP54 T115A mutant Deposited 2020-02-17	Different construct Different mutation/modification 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 1–296（296 aa）	Mutation：T115A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；1M Potassium Citrate	Resolution 2.65 Å R-free 0.309
6Y30 NG domain of human SRP54 T115A mutant Deposited 2020-02-17	Different construct Different mutation/modification 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 1–296（296 aa）	Mutation：T115A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；1M Potassium Citrate	Resolution 2.65 Å R-free 0.309
6Y31 NG domain of human SRP54 T117 deletion mutant Deposited 2020-02-17	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 1–296（296 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.8 M Na2HPO4 , 0.8 M K2HPO4 HEPES 0.1 M (pH 7.5)	Resolution 4.00 Å R-free 0.331
6Y31 NG domain of human SRP54 T117 deletion mutant Deposited 2020-02-17	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 1–296（296 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.8 M Na2HPO4 , 0.8 M K2HPO4 HEPES 0.1 M (pH 7.5)	Resolution 4.00 Å R-free 0.331
6Y31 NG domain of human SRP54 T117 deletion mutant Deposited 2020-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–296（296 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.8 M Na2HPO4 , 0.8 M K2HPO4 HEPES 0.1 M (pH 7.5)	Resolution 4.00 Å R-free 0.331
6Y31 NG domain of human SRP54 T117 deletion mutant Deposited 2020-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–296（296 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.8 M Na2HPO4 , 0.8 M K2HPO4 HEPES 0.1 M (pH 7.5)	Resolution 4.00 Å R-free 0.331
6Y32 Structure of the GTPase heterodimer of human SRP54 and SRalpha Deposited 2020-02-17	Different construct 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 1–296（296 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.4 M lithium sulfate, 13% (w/v) PEG 3350, 0.1 M Tris (pH 8.0)	Resolution 2.60 Å R-free 0.184
6Y32 Structure of the GTPase heterodimer of human SRP54 and SRalpha Deposited 2020-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–296（296 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.4 M lithium sulfate, 13% (w/v) PEG 3350, 0.1 M Tris (pH 8.0)	Resolution 2.60 Å R-free 0.184
6Y32 Structure of the GTPase heterodimer of human SRP54 and SRalpha Deposited 2020-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–296（296 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.4 M lithium sulfate, 13% (w/v) PEG 3350, 0.1 M Tris (pH 8.0)	Resolution 2.60 Å R-free 0.184
6Y32 Structure of the GTPase heterodimer of human SRP54 and SRalpha Deposited 2020-02-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–296（296 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；0.4 M lithium sulfate, 13% (w/v) PEG 3350, 0.1 M Tris (pH 8.0)	Resolution 2.60 Å R-free 0.184
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 x 1–504（504 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 x 1–504（504 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

8 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SRP54_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 11–129； UniProt 323–441

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	1mfq
Deposition date deposition_date	2002-08-13
Structure title title	Crystal Structure Analysis of a Ternary S-Domain Complex of Human Signal Recognition Particle
Keywords keywords	RNA-protein complex, A-minor motif, 3-helix junction, SIGNALING PROTEIN-RNA COMPLEX; SIGNALING 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	33.81 Å
Radius of gyration Rg (electron density) rg_electron	34.60 Å
Forward intensity I(0) i0	150261000.00
Molecular weight molecular_weight	66590.0 kDa
Excluded volume excluded_volume	69857 Å³
Envelope volume envelope_volume	112140 Å³
Hydration-shell volume shell_volume	29944 Å³
Envelope diameter envelope_diameter	129.3 Å
Shell Rg shell_rg	36.77 Å
Envelope Rg envelope_rg	35.00 Å
Shape Rg shape_rg	34.56 Å
Total Rg total_rg	34.80 Å
Total atoms total_atoms	4484
Residues n_residues	342
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	123.1 Å
Rg (real space) rg_real	34.22 Å
Rg uncertainty (real space) rg_real_error	1.57 Å
I(0) (real space) i0_real	1.5030e+08
I(0) uncertainty (real space) i0_real_error	2.9100e+06
Rg (reciprocal space) rg_reciprocal	33.96 Å
I(0) (reciprocal space) i0_reciprocal	150200000.0000
Solution quality estimate total_estimate	0.7822
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.4 Å
Skewness Skewness skewness	0.645
Kurtosis Kurtosis kurtosis	-0.085
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5755000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.634; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.409; Smooth: 0.854

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	7S RNA of human SRP
Molecular weight formula_weight	41566.7 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	4503

GACACUAAGUUCGGCAUCAAUAUGGUGACCUCCCGGGAGCGGGGGACCACCAGGUUGCCUAAGGAGGGGUGAACCGGCCCAGGUCGGAAACGGAGCAGGUCAAAACUCCCGUGCUGAUCAGUAGUGUC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

Entity 2 Entity 2 polymer

Description description	signal recognition particle 19kDa protein
Molecular weight formula_weight	12561.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MRFICIYPAYLNNKKTIAEGRRIPISKAVENPTATEIQDVCSAVGLNVFLEKNKMYSREWNRDVQYRGRVRVQLKQEDGSLCLVQFPSRKSVMLYAAEMIPKLKTRTQ

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 54kDa protein
Molecular weight formula_weight	14733.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MRGSHHHHHHKHGQFTLRDMYEQFQNIMKMGPFSQILGMIPGFGTDFMSKGNEQESMARLKKLMTIMDSMNDQELDSTDGAKVFSKQPGRIQRVARGSGVSTRDVQELLTQYTKFAQMVKKMGGIKGLF

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 BL21(DE3)

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	5

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1mfqb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.201 — SRP19
Superfamily Superfamily superfamily	d.201.1 — SRP19
Family Family family	d.201.1.1 — SRP19

Domain ID domain_id	d1mfqc_
Class class	a — All alpha proteins
Fold Fold fold	a.36 — Signal peptide-binding domain
Superfamily Superfamily superfamily	a.36.1 — Signal peptide-binding domain
Family Family family	a.36.1.1 — Signal peptide-binding domain

CATH v4.4 (2 domains)

Domain ID domain_id	1mfqB00
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	1mfqC00
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 (1)

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Unit-cell length a length_a	131.180 Å
Unit-cell length b length_b	131.180 Å
Unit-cell length c length_c	204.051 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	49.630 Å
R factor r_factor	—
R_work r_work	0.2290
R_free r_free	0.2670

fit	/app/data/saxs_computation/mf/1mfq/1mfq.fit
pddf	/app/data/pr_computation/mf/1mfq/1mfq.pr.out
profile	/app/data/saxs_computation/mf/1mfq/1mfq.dat

Crystal Structure Analysis of a Ternary S-Domain Complex of Human Signal Recognition Particle

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

signal recognition particle 19kDa protein

State in the Current Structure

Other States of the Same Protein in the Database

signal recognition particle 54kDa 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 (6)

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

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)