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2loz

The novel binding mode of DLC1 and Tensin2 PTB domain

Method: SOLUTION NMR Dmax: 48.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tensin-like C1 domain-containing phosphatase

Homo sapiens

UniProt Q63HR2

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 1263–1409 Fragment：PTB domain, UNP residues 1263-1409 Rho GTPase-activating protein 7 × 1 （Q96QB1） SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition：0.6-0.8 mM [U-100% 13C; U-100% 15N] Tensin2-1, 1.2-1.4 mM DLC1-2, 100 mM potassium phosphate-3, 100 mM potassium chloride-4, 1 mM EDTA-5, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1.2-1.4 mM Tensin2-6, 0.6-0.8 mM [U-100% 13C; U-100% 15N] DLC1-7, 100 mM potassium phosphate-8, 100 mM potassium chloride-9, 1 mM EDTA-10, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.6-0.8 mM [U-100% 13C] Tensin2-11, 1.2-1.4 mM DLC1-12, 100 mM potassium phosphate-13, 100 mM potassium chloride-14, 1 mM EDTA-15, 100% D2O | 100% D2O NMR sample composition：1.2-1.4 mM Tensin2-16, 0.6-0.8 mM [U-100% 13C] DLC1-17, 100 mM potassium phosphate-18, 100 mM potassium chloride-19, 1 mM EDTA-20, 100% D2O | 100% D2O Resolution not provided

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 2LOZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2KNO NMR Solution Structure of SH2 Domain of the Human Tensin Like C1 Domain Containing Phosphatase (TENC1) Deposited 2009-08-27 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1135–1249（115 aa） Fragment：Src Homolog 2 domain of TENC1, UNP residues 1135-1249
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient
NMR sample composition 1mM [U-100% 13C] SH2-1, 100mM sodium acetate-2, 100mM sodium chloride-3, 100% D2O | 100% D2O
NMR sample composition 1mM [U-100% 15N] SH2-4, 100mM sodium acetate-5, 100mM sodium chloride-6, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM [U-100% 13C; U-100% 15N] SH2-7, 100mM sodium acetate-8, 100mM sodium chloride-9, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM SH2-10, 100mM sodium acetate-11, 100mM sodium chloride-12, 100% D2O | 100% D2O
Resolution not provided
2L6K Solution Structure of a Nonphosphorylated Peptide Recognizing Domain Deposited 2010-11-22 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1135–1248（114 aa） Fragment：Nonphosphorylated Peptide Recognizing Domain, SH2 domain, UNP residues 2-115
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；293 K；Ionic strength (raw mmCIF value) 150；Pressure ambient
NMR sample composition 0.6mM [U-99% 13C; U-99% 15N] Protein Domain; 150mM sodium chloride; 20mM sodium phosphate; 2mM EDTA; 50mM Arginine; 50mM glutamine; 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3HQC Crystal structure of Phosphotyrosine-binding domain from the Human Tensin-like C1 domain-containing phosphatase (TENC1) Deposited 2009-06-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1264–1409（146 aa） Fragment：Phosphotyrosine Binding Domain, PTB, residues 1264-1409
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 ACT ACETATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4；294 K；100mM Sodium Acetate pH 4 + 2% Glycerol + 2000mM Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Resolution 1.80 Å R-free 0.242

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TENC1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–147； UniProt 1263–1409

Rho GTPase-activating protein 7

Homo sapiens

UniProt Q96QB1

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 811–824 Fragment：UNP residues 811-824 Tensin-like C1 domain-containing phosphatase × 1 （Q63HR2） SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition：0.6-0.8 mM [U-100% 13C; U-100% 15N] Tensin2-1, 1.2-1.4 mM DLC1-2, 100 mM potassium phosphate-3, 100 mM potassium chloride-4, 1 mM EDTA-5, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1.2-1.4 mM Tensin2-6, 0.6-0.8 mM [U-100% 13C; U-100% 15N] DLC1-7, 100 mM potassium phosphate-8, 100 mM potassium chloride-9, 1 mM EDTA-10, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.6-0.8 mM [U-100% 13C] Tensin2-11, 1.2-1.4 mM DLC1-12, 100 mM potassium phosphate-13, 100 mM potassium chloride-14, 1 mM EDTA-15, 100% D2O | 100% D2O NMR sample composition：1.2-1.4 mM Tensin2-16, 0.6-0.8 mM [U-100% 13C] DLC1-17, 100 mM potassium phosphate-18, 100 mM potassium chloride-19, 1 mM EDTA-20, 100% D2O | 100% D2O Resolution not provided

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 2LOZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2DKY Solution structure of the SAM-domain of Rho-GTPase-activating protein 7 Deposited 2006-04-14 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–78（78 aa） Fragment：SAM-domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure AMBIENT
NMR sample composition 1.08mM SAM DOMAIN, 20mM d-TRIS-HCL, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2GYT Solution structure of the SAM (sterile alpha motif) domain of DLC1 (deleted in liver cancer 1) Deposited 2006-05-10 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa） Fragment：sterile alpha motif (SAM) domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate；Pressure 1
NMR sample composition 1mM DLC1-SAM 15N, 13C-labaled; 50mM sodium phosphate buffer(pH 7.0); 3mM DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1mM DLC1-SAM 15N-labaled; 50mM sodium phosphate buffer(pH 7.0); 3mM DTT; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2KAP Solution structure of DLC1-SAM Deposited 2008-11-12 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 17–76（60 aa） Fragment：sterile alpha motif (SAM) domain, UNP residues 17-76
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Pressure ambient
NMR sample composition 1mM DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 5% [U-100% 2H] D2O, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1mM [U-100% 15N] DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 5% [U-100% 2H] D2O, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1mM [U-100% 13C; U-100% 15N] DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 5% [U-100% 2H] D2O, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1mM DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 100 % D2O, 100% D2O | 100% D2O
NMR sample composition 1mM [U-100% 13C; U-100% 15N] DLC1-SAM, 50mM sodium phosphate, 3mM DTT, 100% D2O, 100% D2O | 100% D2O
Resolution not provided
3KUQ Crystal structure of the DLC1 RhoGAP domain Deposited 2009-11-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1066–1275（210 aa） Fragment：Rho-GAP domain
Not recorded UNX UNKNOWN LIGAND × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；291 K；30% PEG-3350, 0.2M sodium chloride, 5% glycerol, 0.02M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP
Resolution 2.30 Å R-free 0.260
5FZT The crystal structure of R7R8 in complex with a DLC1 fragment. Deposited 2016-03-15 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 467–489（23 aa） Fragment：TBS, UNP RESIDUES 467-489
Not recorded MLI MALONATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；15% ETHANOL, 0.1 M TRIS PH 7.4 AT 4OC
Resolution 2.10 Å R-free 0.231

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RHG07_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–14； UniProt 811–824

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 2loz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2loz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2loz
Deposition date deposition_date2012-01-29
Structure title titleThe novel binding mode of DLC1 and Tensin2 PTB domain
Keywords keywordsPTB, DLC1, HYDROLASE-HYDROLASE ACTIVATOR complex; HYDROLASE/HYDROLASE ACTIVATOR
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.43 Å
Radius of gyration Rg (electron density) rg_electron14.88 Å
Forward intensity I(0) i0435479000.00
Molecular weight molecular_weight175240.0 kDa
Excluded volume excluded_volume219280 ų
Envelope volume envelope_volume35038 ų
Hydration-shell volume shell_volume17476 ų
Envelope diameter envelope_diameter51.0 Å
Shell Rg shell_rg22.96 Å
Envelope Rg envelope_rg16.70 Å
Shape Rg shape_rg14.85 Å
Total Rg total_rg15.22 Å
Total atoms total_atoms24690
Residues n_residues1610
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 dmax48.8 Å
Rg (real space) rg_real15.31 Å
Rg uncertainty (real space) rg_real_error0.31 Å
I(0) (real space) i0_real4.3550e+08
I(0) uncertainty (real space) i0_real_error4.6790e+06
Rg (reciprocal space) rg_reciprocal15.32 Å
I(0) (reciprocal space) i0_reciprocal435500000.0000
Solution quality estimate total_estimate0.8907
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.0 Å
Skewness Skewness skewness0.044
Kurtosis Kurtosis kurtosis-0.447
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha728400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.997
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2loza_
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.2 — Phosphotyrosine-binding domain (PTB)

CATH v4.4 (1 domains)

Domain ID domain_id2lozA00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
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8. Citations (1)

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9. Files and Curves (10)