1foe

CRYSTAL STRUCTURE OF RAC1 IN COMPLEX WITH THE GUANINE NUCLEOTIDE EXCHANGE REGION OF TIAM1

Method: X-RAY DIFFRACTION Dmax: 150.2 Å Quality: GOOD

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

T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1

Mus musculus

UniProt Q60610

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 1030–1406 Fragment:RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN Mutation:ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS Non-standard monomer:Yes (specific site not provided by mmCIF) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE × 1 (P63000) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K Resolution 2.80 Å R-free 0.293
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1030–1406 Fragment:RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN Mutation:ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS Non-standard monomer:Yes (specific site not provided by mmCIF) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE × 1 (P63000) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K Resolution 2.80 Å R-free 0.293
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 1030–1406 Fragment:RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN Mutation:ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS Non-standard monomer:Yes (specific site not provided by mmCIF) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE × 1 (P63000) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K Resolution 2.80 Å R-free 0.293
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 1030–1406 Fragment:RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN Mutation:ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS Non-standard monomer:Yes (specific site not provided by mmCIF) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE × 1 (P63000) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K Resolution 2.80 Å R-free 0.293
5 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 1030–1406 Chain C; UniProt 1030–1406 Chain E; UniProt 1030–1406 Chain G; UniProt 1030–1406 Fragment:RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN Mutation:ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS Non-standard monomer:Yes (specific site not provided by mmCIF) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE × 4 (P63000) SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K Resolution 2.80 Å R-free 0.293
6 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1030–1406 Chain G; UniProt 1030–1406 Fragment:RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN Mutation:ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS Non-standard monomer:Yes (specific site not provided by mmCIF) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE × 2 (P63000) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K Resolution 2.80 Å R-free 0.293
7 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1030–1406 Chain E; UniProt 1030–1406 Fragment:RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN Mutation:ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS Non-standard monomer:Yes (specific site not provided by mmCIF) RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE × 2 (P63000) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K Resolution 2.80 Å R-free 0.293

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.

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

View Construct and Data Evidence
UniProt name TIAM1_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–377; UniProt 1030–1406 Author chain C; PDBConstruct 1–377; UniProt 1030–1406 Author chain E; PDBConstruct 1–377; UniProt 1030–1406 Author chain G; PDBConstruct 1–377; UniProt 1030–1406

RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE

Homo sapiens

UniProt P63000

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 1–177 Fragment:RESIDUES 1 TO 177 FROM HUMAN RAC1 T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 × 1 (Q60610) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K Resolution 2.80 Å R-free 0.293
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1–177 Fragment:RESIDUES 1 TO 177 FROM HUMAN RAC1 T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 × 1 (Q60610) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K Resolution 2.80 Å R-free 0.293
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 1–177 Fragment:RESIDUES 1 TO 177 FROM HUMAN RAC1 T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 × 1 (Q60610) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K Resolution 2.80 Å R-free 0.293
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 1–177 Fragment:RESIDUES 1 TO 177 FROM HUMAN RAC1 T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 × 1 (Q60610) SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K Resolution 2.80 Å R-free 0.293
5 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 1–177 Chain D; UniProt 1–177 Chain F; UniProt 1–177 Chain H; UniProt 1–177 Fragment:RESIDUES 1 TO 177 FROM HUMAN RAC1 T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 × 4 (Q60610) SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K Resolution 2.80 Å R-free 0.293
6 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 1–177 Chain H; UniProt 1–177 Fragment:RESIDUES 1 TO 177 FROM HUMAN RAC1 T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 × 2 (Q60610) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K Resolution 2.80 Å R-free 0.293
7 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 1–177 Chain F; UniProt 1–177 Fragment:RESIDUES 1 TO 177 FROM HUMAN RAC1 T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 × 2 (Q60610) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6;277 K;PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K Resolution 2.80 Å R-free 0.293

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.

74 other PDB entries and 96 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAC1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–177; UniProt 1–177 Author chain D; PDBConstruct 1–177; UniProt 1–177 Author chain F; PDBConstruct 1–177; UniProt 1–177 Author chain H; PDBConstruct 1–177; UniProt 1–177

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 1foe

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1foe
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1foe
Deposition date deposition_date2000-08-27
Structure title titleCRYSTAL STRUCTURE OF RAC1 IN COMPLEX WITH THE GUANINE NUCLEOTIDE EXCHANGE REGION OF TIAM1
Keywords keywords;DBL HOMOLOGY DOMAIN, PLECKSTRIN HOMOLOGY DOMAIN, GTPASE, GUANINE NUCLEOTIDE EXCHANGE FACTOR, signaling protein, immune system-signaling protein COMPLEX ;; signaling protein, immune system/signaling protein
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier45.87
Radius of gyration Rg (electron density) rg_electron45.74
Forward intensity I(0) i0865703000.00
Molecular weight molecular_weight249440.0 kDa
Excluded volume excluded_volume314730 ų
Envelope volume envelope_volume442050 ų
Hydration-shell volume shell_volume80888 ų
Envelope diameter envelope_diameter158.5
Shell Rg shell_rg50.16
Envelope Rg envelope_rg44.32
Shape Rg shape_rg45.72
Total Rg total_rg45.99
Total atoms total_atoms17477
Residues n_residues2152
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax150.2
Rg (real space) rg_real45.82
Rg uncertainty (real space) rg_real_error1.21
I(0) (real space) i0_real8.6570e+08
I(0) uncertainty (real space) i0_real_error1.6210e+07
Rg (reciprocal space) rg_reciprocal45.87
I(0) (reciprocal space) i0_reciprocal865700000.0000
Solution quality estimate total_estimate0.8723
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.0
Skewness Skewness skewness0.308
Kurtosis Kurtosis kurtosis-0.393
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha117000000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.673

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1foea1
Class classa — All alpha proteins
Fold Fold folda.87 — DBL homology domain (DH-domain)
Superfamily Superfamily superfamilya.87.1 — DBL homology domain (DH-domain)
Family Family familya.87.1.1 — DBL homology domain (DH-domain)
Domain ID domain_idd1foea2
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.1 — Pleckstrin-homology domain (PH domain)
Domain ID domain_idd1foeb_
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.37.1.8 — G proteins
Domain ID domain_idd1foec1
Class classa — All alpha proteins
Fold Fold folda.87 — DBL homology domain (DH-domain)
Superfamily Superfamily superfamilya.87.1 — DBL homology domain (DH-domain)
Family Family familya.87.1.1 — DBL homology domain (DH-domain)
Domain ID domain_idd1foec2
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.1 — Pleckstrin-homology domain (PH domain)
Domain ID domain_idd1foed_
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.37.1.8 — G proteins
Domain ID domain_idd1foee1
Class classa — All alpha proteins
Fold Fold folda.87 — DBL homology domain (DH-domain)
Superfamily Superfamily superfamilya.87.1 — DBL homology domain (DH-domain)
Family Family familya.87.1.1 — DBL homology domain (DH-domain)
Domain ID domain_idd1foee2
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.1 — Pleckstrin-homology domain (PH domain)
Domain ID domain_idd1foef_
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.37.1.8 — G proteins
Domain ID domain_idd1foeg1
Class classa — All alpha proteins
Fold Fold folda.87 — DBL homology domain (DH-domain)
Superfamily Superfamily superfamilya.87.1 — DBL homology domain (DH-domain)
Family Family familya.87.1.1 — DBL homology domain (DH-domain)
Domain ID domain_idd1foeg2
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.1 — Pleckstrin-homology domain (PH domain)
Domain ID domain_idd1foeh_
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.37.1.8 — G proteins

CATH v4.4 (12 domains)

Domain ID domain_id1foeA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily10 — Dbl homology (DH) domain
Domain ID domain_id1foeA02
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)
Domain ID domain_id1foeB00
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_id1foeC01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily10 — Dbl homology (DH) domain
Domain ID domain_id1foeC02
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)
Domain ID domain_id1foeD00
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_id1foeE01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily10 — Dbl homology (DH) domain
Domain ID domain_id1foeE02
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)
Domain ID domain_id1foeF00
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_id1foeG01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology900 — Dbl Homology Domain; Chain A
Homologous superfamily homologous superfamily10 — Dbl homology (DH) domain
Domain ID domain_id1foeG02
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)
Domain ID domain_id1foeH00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases

8. Citations (1)

9. Files and Curves (10)