SAXSdb — 8qvw

▼

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

Signal recognition particle subunit SRP68

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 52–627	Not recorded	Signal recognition particle subunit SRP72 × 1 （O76094）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

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 8QVW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4P3E Structure of the human SRP S domain Deposited 2014-03-07	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 × 2 PDB declaration: trimeric	Chain C 47–254（208 aa） Fragment：UNP residues 47-254	Mutation：E108D	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
4P3F Structure of the human SRP68-RBD Deposited 2014-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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
8QVX Structure of the PBD of human SRP68/72 (cryoSPARC 3DFlex) Deposited 2023-10-18	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–577； UniProt 52–627

Signal recognition particle subunit SRP72

Homo sapiens

UniProt O76094

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 1–671	Not recorded	Signal recognition particle subunit SRP68 × 1 （Q9UHB9）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.00 Å

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 8QVW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5M72 Structure of the human SRP68-72 protein-binding domain complex Deposited 2016-10-26	Different construct 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 10–166（157 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain D 512–668（157 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 method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain H 512–668（157 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–163（163 aa） Fragment：UNP residues 1-163	Not recorded	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
5WRW Structure of human apo-SRP72 Deposited 2016-12-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–163（163 aa） Fragment：UNP residues 1-163 Chain B 1–163（163 aa） Fragment：UNP residues 1-163	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；(NH4)2SO4	Resolution 2.91 Å R-free 0.266
5WRW Structure of human apo-SRP72 Deposited 2016-12-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–163（163 aa） Fragment：UNP residues 1-163 Chain D 1–163（163 aa） Fragment：UNP residues 1-163	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；(NH4)2SO4	Resolution 2.91 Å R-free 0.266
5WRW Structure of human apo-SRP72 Deposited 2016-12-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–163（163 aa） Fragment：UNP residues 1-163 Chain F 1–163（163 aa） Fragment：UNP residues 1-163	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；(NH4)2SO4	Resolution 2.91 Å R-free 0.266
7NFX Mammalian ribosome nascent chain complex with SRP and SRP receptor in early state A Deposited 2021-02-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 55-meric	Chain z 1–671（671 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
8QVX Structure of the PBD of human SRP68/72 (cryoSPARC 3DFlex) Deposited 2023-10-18	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–671（671 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

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

View Construct and Data Evidence

UniProt name	SRP72_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–674； UniProt 1–671

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8qvw
Deposition date deposition_date	2023-10-18
Structure title title	Cryo-EM structure of the peptide binding domain of human SRP68/72
Keywords keywords	Signal recognition particle, TPR, protein translocation, TRANSLATION; TRANSLATION
Experimental Method method	ELECTRON MICROSCOPY

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	29.88 Å
Radius of gyration Rg (electron density) rg_electron	29.74 Å
Forward intensity I(0) i0	49633600.00
Molecular weight molecular_weight	55726.0 kDa
Excluded volume excluded_volume	70161 Å³
Envelope volume envelope_volume	90880 Å³
Hydration-shell volume shell_volume	27859 Å³
Envelope diameter envelope_diameter	112.9 Å
Shell Rg shell_rg	33.62 Å
Envelope Rg envelope_rg	29.86 Å
Shape Rg shape_rg	29.73 Å
Total Rg total_rg	30.14 Å
Total atoms total_atoms	3918
Residues n_residues	492
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	107.6 Å
Rg (real space) rg_real	30.15 Å
Rg uncertainty (real space) rg_real_error	1.15 Å
I(0) (real space) i0_real	4.9630e+07
I(0) uncertainty (real space) i0_real_error	7.8230e+05
Rg (reciprocal space) rg_reciprocal	30.03 Å
I(0) (reciprocal space) i0_reciprocal	49630000.0000
Solution quality estimate total_estimate	0.8282
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.4 Å
Skewness Skewness skewness	0.592
Kurtosis Kurtosis kurtosis	-0.008
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7648000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.719; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.734; Smooth: 0.872

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Signal recognition particle subunit SRP68
Molecular weight formula_weight	66617.3 kDa
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	3918

MKEFGDSLSLEILQIIKESQQQHGLRHGDFQRYRGYCSRRQRRLRKTLNFKMGNRHKFTGKKVTEELLTDNRYLLLVLMDAERAWSYAMQLKQEANTEPRKRFHLLSRLRKAVKHAEELERLCESNRVDAKTKLEAQAYTAYLSGMLRFEHQEWKAAIEAFNKCKTIYEKLASAFTEEQAVLYNQRVEEISPNIRYCAYNIGDQSAINELMQMRLRSGGTEGLLAEKLEALITQTRAKQAATMSEVEWRGRTVPVKIDKVRIFLLGLADNEAAIVQAESEETKERLFESMLSECRDAIQVVREELKPDQKQRDYILEGEPGKVSNLQYLHSYLTYIKLSTAIKRNENMAKGLQRALLQQQPEDDSKRSPRPQDLIRLYDIILQNLVELLQLPGLEEDKAFQKEIGLKTLVFKAYRCFFIAQSYVLVKKWSEALVLYDRVLKYANEVNSDAGAFKNSLKDLPDVQELITQVRSEKCSLQAAAILDANDAHQTETSSSQVKDNKPLVERFETFCLDPSLVTKQANLVHFPPGFQPIPCKPLFFDLALNHVAFPPLEDKLEQKTKSGLTGYIKGIFGFRS

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 2 Entity 2 polymer

Description description	Signal recognition particle subunit SRP72
Molecular weight formula_weight	74992.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SNAMASGGSGGVSVPALWSEVNRYGQNGDFTRALKTVNKILQINKDDVTALHCKVVCLIQNGSFKEALNVINTHTKVLANNSLSFEKAYCEYRLNRIENALKTIESANQQTDKLKELYGQVLYRLERYDECLAVYRDLVRNSQDDYDEERKTNLSAVVAAQSNWEKVVPENLGLQEGTHELCYNTACALIGQGQLNQAMKILQKAEDLCRRSLSEDTDGTEEDPQAELAIIHGQMAYILQLQGRTEEALQLYNQIIKLKPTDVGLLAVIANNIITINKDQNVFDSKKKVKLTNAEGVEFKLSKKQLQAIEFNKALLAMYTNQAEQCRKISASLQSQSPEHLLPVLIQAAQLCREKQHTKAIELLQEFSDQHPENAAEIKLTMAQLKISQGNISKACLILRSIEELKHKPGMVSALVTMYSHEEDIDSAIEVFTQAIQWYQNHQPKSPAHLSLIREAANFKLKYGRKKEAISDLQQLWKQNPKDIHTLAQLISAYSLVDPEKAKALSKHLPSSDSMSLKVDVEALENSAGATYIRKKGGKVTGDSQPKEQGQGDLKKKKKKKKGKLPKNYDPKVTPDPERWLPMRERSYYRGRKKGKKKDQIGKGTQGATAGASSELDASKTVSSPPTSPRPGSAATVSASTSNIIPPRHQKPAGAPATKKKQQQKKKKGGKGGW

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

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	38514

fit	/app/data/saxs_computation/qv/8qvw/8qvw.fit
pddf	/app/data/pr_computation/qv/8qvw/8qvw.pr.out
profile	/app/data/saxs_computation/qv/8qvw/8qvw.dat

Cryo-EM structure of the peptide binding domain of human SRP68/72

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

Signal recognition particle subunit SRP68

State in the Current Structure

Other States of the Same Protein in the Database

Signal recognition particle subunit SRP72

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

冷冻电镜 EM 3D

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)