SAXSdb — 3qwl

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

TBC1 domain family member 7

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–293	Not recorded	UNX UNKNOWN LIGAND × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；20% PEG-1500, 0.2M magnesium chloride, 0.1M TRIS. 1:10 dispase-1 added in situ., pH 8.5, vapor diffusion, sitting drop, temperature 289K X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；Selenomethionyl derivative protein. 30% PEG-1500, 0.2M sodium chloride, 0.1M HEPES. 1:10 dispase-1 added in situ., pH 7.5, vapor diffusion, sitting drop, temperature 289K	Resolution 1.90 Å R-free 0.259

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 3QWL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4Z6Y Structure of the TBC1D7-TSC1 complex Deposited 2015-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 21–293（273 aa） Fragment：UNP RESIDUES 21-293 Chain E 21–293（273 aa） Fragment：UNP RESIDUES 21-293	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；8% PEG 6000, 4% 2-methyl-2,4-pentanediol (MPD), 0.1M HEPES, pH7.5	Resolution 2.81 Å R-free 0.255
4Z6Y Structure of the TBC1D7-TSC1 complex Deposited 2015-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 21–293（273 aa） Fragment：UNP RESIDUES 21-293 Chain G 21–293（273 aa） Fragment：UNP RESIDUES 21-293	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；8% PEG 6000, 4% 2-methyl-2,4-pentanediol (MPD), 0.1M HEPES, pH7.5	Resolution 2.81 Å R-free 0.255
5EJC Crystal structural of the TSC1-TBC1D7 complex Deposited 2015-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 18–293（276 aa） Fragment：UNP residues 18-293	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；200 mM NaCl, 20mM CaCl2 and 15% PEG-3350	Resolution 3.10 Å R-free 0.239
5EJC Crystal structural of the TSC1-TBC1D7 complex Deposited 2015-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 18–293（276 aa） Fragment：UNP residues 18-293	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；200 mM NaCl, 20mM CaCl2 and 15% PEG-3350	Resolution 3.10 Å R-free 0.239
7DL2 Cryo-EM structure of human TSC complex Deposited 2020-11-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain E 21–287（267 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
9CE3 Structure of the TSC:WIPI3 lysosomal recruitment complex Deposited 2024-06-26	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 1–293（293 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES (pH 7.6), 250 mM NaCl, 2 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å

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

View Construct and Data Evidence

UniProt name	TBCD7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–294； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3qwl
Deposition date deposition_date	2011-02-28
Structure title title	Crystal structure of human TBC1 domain family member 7
Keywords keywords	Rab GTPase activation, structural genomics consortium, TBC domain, SGC, HYDROLASE ACTIVATOR; HYDROLASE ACTIVATOR
Experimental Method method	X-RAY DIFFRACTION

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

该条目暂无 SAXS 数据。

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

该条目暂无 P(r) 分析数据。

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	TBC1 domain family member 7
Molecular weight formula_weight	34076.6 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	2195

GMTEDSQRNFRSVYYEKVGFRGVEEKKSLEILLKDDRLDTEKLCTFSQRFPLPSMYRALVWKVLLGILPPHHESHAKVMMYRKEQYLDVLHALKVVRFVSDATPQAEVYLRMYQLESGKLPRSPSFPLEPDDEVFLAIAKAMEEMVEDSVDCYWITRRFVNQLNTKYRDSLPQLPKAFEQYLNLEDGRLLTHLRMCSAAPKLPYDLWFKRCFAGCLPESSLQRVWDKVVSGSCKILVFVAVEILLTFKIKVMALNSAEKITKFLENIPQDSSDAIVSKAIDLWHKHCGTPVHSS

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 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3qwlA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	750 — Ypt/Rab-GAP domain of gyp1p, domain 1

Domain ID domain_id	3qwlA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	680 — Ypt/Rab-GAP domain of gyp1p, domain 2

Domain ID domain_id	3qwlA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	80 — Ypt/Rab-GAP domain of gyp1p, domain 3

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8. Citations (1)

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Unit-cell length a length_a	34.574 Å
Unit-cell length b length_b	83.984 Å
Unit-cell length c length_c	87.684 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2130
R_work r_work	0.2112
R_free r_free	0.2585

Crystal structure of human TBC1 domain family member 7