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1qzw

Crystal structure of the complete core of archaeal SRP and implications for inter-domain communication

Method: X-RAY DIFFRACTION Dmax: 179.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Signal recognition 54 kDa protein

Sulfolobus solfataricus

UniProt Q97ZE7

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 A； UniProt 1–432 Not recorded 7S RNA × 1 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
2 Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts Chain C； UniProt 1–432 Not recorded 7S RNA × 1 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
3 Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts Chain E； UniProt 1–432 Not recorded 7S RNA × 1 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
4 Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts Chain G； UniProt 1–432 Not recorded 7S RNA × 1 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

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 1QZW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1QZX Crystal structure of the complete core of archaeal SRP and implications for inter-domain communication Deposited 2003-09-18 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 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
3KL4 Recognition of a signal peptide by the signal recognition particle Deposited 2009-11-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–432（431 aa） Fragment：UNP residues 2-432
Not recorded No recorded non-water small molecule 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
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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–292（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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–292（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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–292（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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–292（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 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SRP54_SULSO
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 9–440； UniProt 1–432 Author chain C； PDBConstruct 9–440； UniProt 1–432 Author chain E； PDBConstruct 9–440； UniProt 1–432 Author chain G； PDBConstruct 9–440； UniProt 1–432

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1qzw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1qzw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1qzw
Deposition date deposition_date2003-09-18
Structure title titleCrystal structure of the complete core of archaeal SRP and implications for inter-domain communication
Keywords keywordsSignal recognition particle, SRP, ribonucleoprotein complex, protein-RNA complex, protein targeting, Signaling Protein-RNA COMPLEX; Signaling Protein/RNA
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier62.39 Å
Radius of gyration Rg (electron density) rg_electron60.41 Å
Forward intensity I(0) i01272360000.00
Molecular weight molecular_weight256190.0 kDa
Excluded volume excluded_volume303780 ų
Envelope volume envelope_volume575770 ų
Hydration-shell volume shell_volume83305 ų
Envelope diameter envelope_diameter190.6 Å
Shell Rg shell_rg56.07 Å
Envelope Rg envelope_rg58.63 Å
Shape Rg shape_rg60.29 Å
Total Rg total_rg60.64 Å
Total atoms total_atoms17720
Residues n_residues1908
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax179.4 Å
Rg (real space) rg_real62.55 Å
Rg uncertainty (real space) rg_real_error1.15 Å
I(0) (real space) i0_real1.2720e+09
I(0) uncertainty (real space) i0_real_error2.5040e+07
Rg (reciprocal space) rg_reciprocal62.18 Å
I(0) (reciprocal space) i0_reciprocal1271000000.0000
Solution quality estimate total_estimate0.8332
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary64.6 Å
Skewness Skewness skewness0.286
Kurtosis Kurtosis kurtosis-0.689
Angular range angular_range— – 0.1250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41370000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.949; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1qzwa1
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.13 — Domain of the SRP/SRP receptor G-proteins
Family Family familya.24.13.1 — Domain of the SRP/SRP receptor G-proteins
Domain ID domain_idd1qzwa2
Class classa — All alpha proteins
Fold Fold folda.36 — Signal peptide-binding domain
Superfamily Superfamily superfamilya.36.1 — Signal peptide-binding domain
Family Family familya.36.1.1 — Signal peptide-binding domain
Domain ID domain_idd1qzwa3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.10 — Nitrogenase iron protein-like
Domain ID domain_idd1qzwc1
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.13 — Domain of the SRP/SRP receptor G-proteins
Family Family familya.24.13.1 — Domain of the SRP/SRP receptor G-proteins
Domain ID domain_idd1qzwc2
Class classa — All alpha proteins
Fold Fold folda.36 — Signal peptide-binding domain
Superfamily Superfamily superfamilya.36.1 — Signal peptide-binding domain
Family Family familya.36.1.1 — Signal peptide-binding domain
Domain ID domain_idd1qzwc3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.10 — Nitrogenase iron protein-like
Domain ID domain_idd1qzwe1
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.13 — Domain of the SRP/SRP receptor G-proteins
Family Family familya.24.13.1 — Domain of the SRP/SRP receptor G-proteins
Domain ID domain_idd1qzwe2
Class classa — All alpha proteins
Fold Fold folda.36 — Signal peptide-binding domain
Superfamily Superfamily superfamilya.36.1 — Signal peptide-binding domain
Family Family familya.36.1.1 — Signal peptide-binding domain
Domain ID domain_idd1qzwe3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.10 — Nitrogenase iron protein-like
Domain ID domain_idd1qzwg1
Class classa — All alpha proteins
Fold Fold folda.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamilya.24.13 — Domain of the SRP/SRP receptor G-proteins
Family Family familya.24.13.1 — Domain of the SRP/SRP receptor G-proteins
Domain ID domain_idd1qzwg2
Class classa — All alpha proteins
Fold Fold folda.36 — Signal peptide-binding domain
Superfamily Superfamily superfamilya.36.1 — Signal peptide-binding domain
Family Family familya.36.1.1 — Signal peptide-binding domain
Domain ID domain_idd1qzwg3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.10 — Nitrogenase iron protein-like
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8. Citations (1)

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9. Files and Curves (10)