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5l3v

Structure of the crenarchaeal SRP54 GTPase bound to GDP

Method: X-RAY DIFFRACTION Dmax: 99.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Signal recognition particle 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–293 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–293 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

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 5L3V 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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

5 other PDB entries and 12 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 7–299； UniProt 1–293 Author chain B； PDBConstruct 7–299； UniProt 1–293

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 5l3v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5l3v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5l3v
Deposition date deposition_date2016-05-24
Structure title titleStructure of the crenarchaeal SRP54 GTPase bound to GDP
Keywords keywordsco-translational protein targeting, Signal Recognition Particle, GTPase, Signaling protein, protein transport; PROTEIN TRANSPORT
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_guinier29.72 Å
Radius of gyration Rg (electron density) rg_electron29.10 Å
Forward intensity I(0) i065774800.00
Molecular weight molecular_weight65404.0 kDa
Excluded volume excluded_volume82792 ų
Envelope volume envelope_volume103710 ų
Hydration-shell volume shell_volume30751 ų
Envelope diameter envelope_diameter101.1 Å
Shell Rg shell_rg35.20 Å
Envelope Rg envelope_rg28.86 Å
Shape Rg shape_rg29.09 Å
Total Rg total_rg29.74 Å
Total atoms total_atoms4599
Residues n_residues583
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 dmax99.9 Å
Rg (real space) rg_real29.80 Å
Rg uncertainty (real space) rg_real_error0.70 Å
I(0) (real space) i0_real6.5770e+07
I(0) uncertainty (real space) i0_real_error8.8300e+05
Rg (reciprocal space) rg_reciprocal29.77 Å
I(0) (reciprocal space) i0_reciprocal65770000.0000
Solution quality estimate total_estimate0.8735
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.3 Å
Skewness Skewness skewness0.395
Kurtosis Kurtosis kurtosis-0.342
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha39390000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.859
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5l3va1
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.24.13.0 — automated matches
Domain ID domain_idd5l3va2
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_idd5l3vb1
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.24.13.0 — automated matches
Domain ID domain_idd5l3vb2
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

CATH v4.4 (4 domains)

Domain ID domain_id5l3vA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily140 — SRP54, nucleotide-binding domain
Domain ID domain_id5l3vA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id5l3vB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily140 — SRP54, nucleotide-binding domain
Domain ID domain_id5l3vB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
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8. Citations (1)

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9. Files and Curves (10)