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9mey

Crystal structure of RIT1(GDP) bound to LZTR1(Kelch domain)

Method: X-RAY DIFFRACTION Dmax: 121.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

GTP-binding protein Rit1

Homo sapiens

UniProt Q92963

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 2–197 Not recorded Leucine-zipper-like transcriptional regulator 1 × 1 （Q8N653） GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.2；277 K；44% Morpheus II PPT7, 100mM MonoSach II, 100mM MB6 buffer pH 8.2 Resolution 2.95 Å R-free 0.256
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 2–197 Not recorded Leucine-zipper-like transcriptional regulator 1 × 1 （Q8N653） GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.2；277 K；44% Morpheus II PPT7, 100mM MonoSach II, 100mM MB6 buffer pH 8.2 Resolution 2.95 Å R-free 0.256

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 9MEY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4KLZ Inhibition of Small GTPases by Stabilization of the GDP Complex, a Novel Approach applied to Rit1, a Target for Rheumatoid Arthritis Deposited 2013-05-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 19–189（171 aa） Fragment：GTP binding domain, unp residues 19-189
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；11-14% w/v PEG4000, 5-8% v/v Jeffamine M600, imidazole , VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 2.30 Å R-free 0.311
9MF1 Crystal structure of RIT1 in the GDP state Deposited 2024-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–197（196 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；10% w/v PEG 6000, 0.1M Bicine pH 9.0
Resolution 2.20 Å R-free 0.230

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RIT1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–197； UniProt 2–197 Author chain C； PDBConstruct 2–197； UniProt 2–197

Leucine-zipper-like transcriptional regulator 1

Homo sapiens

UniProt Q8N653

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 50–329 Chain B； UniProt 382–422 Not recorded GTP-binding protein Rit1 × 1 （Q92963） GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.2；277 K；44% Morpheus II PPT7, 100mM MonoSach II, 100mM MB6 buffer pH 8.2 Resolution 2.95 Å R-free 0.256
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 50–329 Chain D； UniProt 382–422 Not recorded GTP-binding protein Rit1 × 1 （Q92963） GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.2；277 K；44% Morpheus II PPT7, 100mM MonoSach II, 100mM MB6 buffer pH 8.2 Resolution 2.95 Å R-free 0.256

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 9MEY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9MEZ Crystal structure of MRAS(GDP) bound to LZTR1(Kelch domain) Deposited 2024-12-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 50–331（282 aa）
Chain B 384–422（39 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；11.2% w/v PEG3350, 5.26% Tacsimate pH 6.0
Resolution 2.80 Å R-free 0.255
9MEZ Crystal structure of MRAS(GDP) bound to LZTR1(Kelch domain) Deposited 2024-12-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 50–331（282 aa）
Chain D 384–422（39 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 MLA MALONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；11.2% w/v PEG3350, 5.26% Tacsimate pH 6.0
Resolution 2.80 Å R-free 0.255
9MEZ Crystal structure of MRAS(GDP) bound to LZTR1(Kelch domain) Deposited 2024-12-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 50–331（282 aa）
Chain F 384–422（39 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 MLA MALONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；11.2% w/v PEG3350, 5.26% Tacsimate pH 6.0
Resolution 2.80 Å R-free 0.255
9MEZ Crystal structure of MRAS(GDP) bound to LZTR1(Kelch domain) Deposited 2024-12-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 50–331（282 aa）
Chain H 384–422（39 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 MLA MALONIC ACID × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；11.2% w/v PEG3350, 5.26% Tacsimate pH 6.0
Resolution 2.80 Å R-free 0.255
9MEZ Crystal structure of MRAS(GDP) bound to LZTR1(Kelch domain) Deposited 2024-12-09 Different construct Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 50–331（282 aa）
Chain J 384–422（39 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；11.2% w/v PEG3350, 5.26% Tacsimate pH 6.0
Resolution 2.80 Å R-free 0.255
9MF0 Crystal structure of KRAS(GDP) bound to LZTR1(Kelch domain) Deposited 2024-12-09 Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 50–329（280 aa）
Chain B 382–422（41 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；8% w/v PGA-LM. 0.3M sodium malonate dibasic monohydrate, 0.1M sodium acetate pH 5.0.
Resolution 3.30 Å R-free 0.233
9MF0 Crystal structure of KRAS(GDP) bound to LZTR1(Kelch domain) Deposited 2024-12-09 Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 50–329（280 aa）
Chain D 382–422（41 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；8% w/v PGA-LM. 0.3M sodium malonate dibasic monohydrate, 0.1M sodium acetate pH 5.0.
Resolution 3.30 Å R-free 0.233
9MF0 Crystal structure of KRAS(GDP) bound to LZTR1(Kelch domain) Deposited 2024-12-09 Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 50–329（280 aa）
Chain F 382–422（41 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；8% w/v PGA-LM. 0.3M sodium malonate dibasic monohydrate, 0.1M sodium acetate pH 5.0.
Resolution 3.30 Å R-free 0.233
9MF0 Crystal structure of KRAS(GDP) bound to LZTR1(Kelch domain) Deposited 2024-12-09 Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 50–329（280 aa）
Chain H 382–422（41 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；8% w/v PGA-LM. 0.3M sodium malonate dibasic monohydrate, 0.1M sodium acetate pH 5.0.
Resolution 3.30 Å R-free 0.233
9MF0 Crystal structure of KRAS(GDP) bound to LZTR1(Kelch domain) Deposited 2024-12-09 Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 50–329（280 aa）
Chain J 382–422（41 aa）
Not recorded MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；8% w/v PGA-LM. 0.3M sodium malonate dibasic monohydrate, 0.1M sodium acetate pH 5.0.
Resolution 3.30 Å R-free 0.233

2 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LZTR1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–281； UniProt 50–329 Author chain B； PDBConstruct 282–322； UniProt 382–422 Author chain D； PDBConstruct 2–281； UniProt 50–329 Author chain D； PDBConstruct 282–322； UniProt 382–422

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 9mey

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9mey
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9mey
Deposition date deposition_date2024-12-09
Structure title titleCrystal structure of RIT1(GDP) bound to LZTR1(Kelch domain)
Keywords keywordsSubstrate adaptor, ONCOPROTEIN; ONCOPROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.37 Å
Radius of gyration Rg (electron density) rg_electron36.16 Å
Forward intensity I(0) i0206970000.00
Molecular weight molecular_weight113350.0 kDa
Excluded volume excluded_volume140410 ų
Envelope volume envelope_volume180620 ų
Hydration-shell volume shell_volume42801 ų
Envelope diameter envelope_diameter126.2 Å
Shell Rg shell_rg41.08 Å
Envelope Rg envelope_rg35.89 Å
Shape Rg shape_rg36.14 Å
Total Rg total_rg36.53 Å
Total atoms total_atoms7988
Residues n_residues994
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 dmax121.4 Å
Rg (real space) rg_real36.50 Å
Rg uncertainty (real space) rg_real_error1.20 Å
I(0) (real space) i0_real2.0700e+08
I(0) uncertainty (real space) i0_real_error3.6100e+06
Rg (reciprocal space) rg_reciprocal36.42 Å
I(0) (reciprocal space) i0_reciprocal207000000.0000
Solution quality estimate total_estimate0.8746
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.9 Å
Skewness Skewness skewness0.382
Kurtosis Kurtosis kurtosis-0.500
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha48200000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.878; Smooth: 0.863
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)