SAXSdb — 4arz

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

GTP-BINDING PROTEIN GTR1

SACCHAROMYCES CEREVISIAE

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 1–310	Not recorded	GTP-BINDING PROTEIN GTR2 × 1 （P53290） GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；pH 8.5	Resolution 3.10 Å R-free 0.272

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 4ARZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3R7W Crystal Structure of Gtr1p-Gtr2p complex Deposited 2011-03-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 8–310（303 aa） Fragment：residues 8-310	Non-standard monomer：Yes (specific site not provided by mmCIF)	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1M HEPES, 10% PEG monomethyl ether 5000, 5%(v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.77 Å R-free 0.283
3R7W Crystal Structure of Gtr1p-Gtr2p complex Deposited 2011-03-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 8–310（303 aa） Fragment：residues 8-310	Non-standard monomer：Yes (specific site not provided by mmCIF)	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1M HEPES, 10% PEG monomethyl ether 5000, 5%(v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.77 Å R-free 0.283
6JWP crystal structure of EGOC Deposited 2019-04-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–310（310 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000	Resolution 3.20 Å R-free 0.285
6JWP crystal structure of EGOC Deposited 2019-04-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 1–310（310 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000	Resolution 3.20 Å R-free 0.285
9H4Q Cryo-EM structure of the SEAC wing - EGOC Deposited 2024-10-21	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain a 1–310（310 aa）	Not recorded	MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9H5K Cryo-EM structure of the SEAC-EGOC supercomplex Deposited 2024-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain a 1–310（310 aa） Chain b 1–310（310 aa）	Not recorded	ZN ZINC ION × 28 MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

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

View Construct and Data Evidence

UniProt name	GTR1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–310； UniProt 1–310

GTP-BINDING PROTEIN GTR2

SACCHAROMYCES CEREVISIAE

UniProt P53290

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 1–341	Not recorded	GTP-BINDING PROTEIN GTR1 × 1 （Q00582） GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；pH 8.5	Resolution 3.10 Å R-free 0.272

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 4ARZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3R7W Crystal Structure of Gtr1p-Gtr2p complex Deposited 2011-03-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–341（331 aa） Fragment：residues 11-341	Non-standard monomer：Yes (specific site not provided by mmCIF)	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1M HEPES, 10% PEG monomethyl ether 5000, 5%(v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.77 Å R-free 0.283
3R7W Crystal Structure of Gtr1p-Gtr2p complex Deposited 2011-03-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 11–341（331 aa） Fragment：residues 11-341	Non-standard monomer：Yes (specific site not provided by mmCIF)	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1M HEPES, 10% PEG monomethyl ether 5000, 5%(v/v) Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.77 Å R-free 0.283
6JWP crystal structure of EGOC Deposited 2019-04-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–341（341 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000	Resolution 3.20 Å R-free 0.285
6JWP crystal structure of EGOC Deposited 2019-04-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain G 1–341（341 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；100mM HEPES (pH 7.5), 200mM NaCl, and 12%(w/v) PEG 8000	Resolution 3.20 Å R-free 0.285
9H4Q Cryo-EM structure of the SEAC wing - EGOC Deposited 2024-10-21	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain c 1–341（341 aa）	Not recorded	MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9H5K Cryo-EM structure of the SEAC-EGOC supercomplex Deposited 2024-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 32 PDB declaration: 32-meric	Chain c 1–341（341 aa） Chain d 1–341（341 aa）	Not recorded	ZN ZINC ION × 28 MG MAGNESIUM ION × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

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

View Construct and Data Evidence

UniProt name	GTR2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–341； UniProt 1–341

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	4arz
Deposition date deposition_date	2012-04-27
Structure title title	The crystal structure of Gtr1p-Gtr2p complexed with GTP-GDP
Keywords keywords	HYDROLASE, GTPASE, CELL GROWTH; 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	28.40 Å
Radius of gyration Rg (electron density) rg_electron	27.57 Å
Forward intensity I(0) i0	75307000.00
Molecular weight molecular_weight	69331.0 kDa
Excluded volume excluded_volume	87387 Å³
Envelope volume envelope_volume	105910 Å³
Hydration-shell volume shell_volume	31888 Å³
Envelope diameter envelope_diameter	88.7 Å
Shell Rg shell_rg	34.83 Å
Envelope Rg envelope_rg	27.54 Å
Shape Rg shape_rg	27.58 Å
Total Rg total_rg	28.31 Å
Total atoms total_atoms	4861
Residues n_residues	595
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	89.4 Å
Rg (real space) rg_real	28.33 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	7.5310e+07
I(0) uncertainty (real space) i0_real_error	1.2390e+06
Rg (reciprocal space) rg_reciprocal	28.35 Å
I(0) (reciprocal space) i0_reciprocal	75310000.0000
Solution quality estimate total_estimate	0.9081
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.3 Å
Skewness Skewness skewness	0.227
Kurtosis Kurtosis kurtosis	-0.572
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	21860000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.972

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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	GTP-BINDING PROTEIN GTR1
Molecular weight formula_weight	35892.5 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	4870

MSSNNRKKLLLMGRSGSGKSSMRSIIFSNYSAFDTRRLGATIDVEHSHLRFLGNMTLNLWDCGGQDVFMENYFTKQKDHIFQMVQVLIHVFDVESTEVLKDIEIFAKALKQLRKYSPDAKIFVLLHKMDLVQLDKREELFQIMMKNLSETSSEFGFPNLIGFPTSIWDESLYKAWSQIVCSLIPNMSNHQSNLKKFKEIMNALEIILFERTTFLVICSSNGENSNENHDSSDNNNVLLDPKRFEKISNIMKNFKQSCTKLKSGFKTLILNNNIYVSELSSNMVCFIVLKDMNIPQELVLENIKKAKEFFQ

来源 Source

来源生物 organism	SACCHAROMYCES CEREVISIAE
通用名 common_name	;BAKER'S YEAST ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	GTP-BINDING PROTEIN GTR2
Molecular weight formula_weight	38634.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSLEATDSKAMVLLMGVRRCGKSSICKVVFHNMQPLDTLYLESTSNPSLEHFSTLIDLAVMELPGQLNYFEPSYDSERLFKSVGALVYVIDSQDEYINAITNLAMIIEYAYKVNPSINIEVLIHKVDGLSEDFKVDAQRDIMQRTGEELLELGLDGVQVSFYLTSIFDHSIYEAFSRIVQKLIPELSFLENMLDNLIQHSKIEKAFLFDVNSKIYVSTDSNPVDIQMYEVCSEFIDVTIDLFDLYKAPVLRNSQKSSDKDNVINPRNELQNVSQLANGVIIYLRQMIRGLALVAIIRPNGTDMESCLTVADYNIDIFKKGLEDIWANARASQAKNSIEDDV

来源 Source

来源生物 organism	SACCHAROMYCES CEREVISIAE
通用名 common_name	;BAKER'S YEAST ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	1

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	1

Entity 5 Entity 5 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4arzA01
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	4arzA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	190 —

Domain ID domain_id	4arzB01
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	4arzB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	450 — Beta-Lactamase
Homologous superfamily homologous superfamily	190 —

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8. Citations (1)

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Unit-cell length a length_a	90.712 Å
Unit-cell length b length_b	148.897 Å
Unit-cell length c length_c	117.759 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2719

fit	/app/data/saxs_computation/ar/4arz/4arz.fit
pddf	/app/data/pr_computation/ar/4arz/4arz.pr.out
profile	/app/data/saxs_computation/ar/4arz/4arz.dat

The crystal structure of Gtr1p-Gtr2p complexed with GTP-GDP

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

GTP-BINDING PROTEIN GTR1

State in the Current Structure

Other States of the Same Protein in the Database

GTP-BINDING PROTEIN GTR2

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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)