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1wxm

Solution Structure of the N-terminal Ras-binding Domain (RBD) in Human a-Raf Kinase

Method: SOLUTION NMR Dmax: 35.1 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

A-Raf proto-oncogene serine/threonine-protein kinase

Homo sapiens

UniProt P10398

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 19–91 Fragment：Ras-binding domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；296 K；Ionic strength (raw mmCIF value) 200mM；Pressure ambient NMR sample composition：0.86mM protein U-15N, 13C; 20mM d-Tris-HCl (pH7.0); 200mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O | 90% H2O/10% 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 1WXM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2MSE NMR data-driven model of GTPase KRas-GNP:ARafRBD complex tethered to a lipid-bilayer nanodisc Deposited 2014-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 19–91（73 aa） Fragment：UNP residues 19-91
Not recorded PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 64 17F O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine × 16 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 0.105；Pressure ambient
NMR sample composition 0.6 mM U-15N, Ile C-delta-13C K-Ras-1, 0.6 mM membrane scaffold protein-2, 0.7 mM A-RafRBD-3, 100 mM sodium chloride-4, 5 mM Magnesium-5, 20 mM TRIS-6, 2 mM TCEP-7, 0.6 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-8, 18.75 mM 1,2-dioleoyl-sn-glycero-3-phosphocholine-9, 5 mM 1,2-dioleoyl-sn-glycero-3-phospho-L-serine-10, 1.25 mM 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-11, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.7 mM K-Ras-12, 0.7 mM membrane scaffold protein-13, 0.6 mM U-15N, Ile C-delta-13C A-RafRBD-14, 5 mM Magnesium-15, 20 mM TRIS-16, 100 mM sodium chloride-17, 2 mM TCEP-18, 0.7 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-19, 18.75 mM 1,2-dioleoyl-sn-glycero-3-phosphocholine-20, 5 mM 1,2-dioleoyl-sn-glycero-3-phospho-L-serine-21, 1.25 mM 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-22, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.6 mM U-15N, Ile C-delta-13C K-Ras-23, 0.7 mM A-RafRBD-24, 0.6 mM membrane scaffold protein-25, 20 mM TRIS-26, 100 mM sodium chloride-27, 5 mM Magnesium-28, 2 mM TCEP-29, 0.6 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-30, 18.75 mM 1,2-dioleoyl-sn-glycero-3-phosphocholine-31, 5 mM 1,2-dioleoyl-sn-glycero-3-phospho-L-serine-32, 1.25 mM 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-33, 0.65 mM 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)-34, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.7 mM K-Ras-35, 0.6 mM U-15N, Ile C-delta-13C A-RafRBD-36, 0.7 mM membrane scaffold protein-37, 20 mM TRIS-38, 100 mM sodium chloride-39, 5 mM Magnesium-40, 2 mM TCEP-41, 0.7 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-42, 18.75 mM 1,2-dioleoyl-sn-glycero-3-phosphocholine-43, 5 mM 1,2-dioleoyl-sn-glycero-3-phospho-L-serine-44, 1.25 mM 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-45, 0.65 mM 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)-46, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
8VSL Binary structure of 14-3-3 sigma and ARAF phosphopeptide (pS214) Deposited 2024-01-24 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 × 4 PDB declaration: tetrameric
Chain P 209–220（12 aa） Fragment：residues 209-220 (Uniprot numbering)
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；PEG400, HEPES, CaCl2, glycerol
Resolution 1.42 Å R-free 0.208
8VSM Ternary structure of 14-3-3 sigma, ARAF phosphopeptide (pS214) and compound 78 (1124378) Deposited 2024-01-24 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 × 4 PDB declaration: tetrameric
Chain P 209–220（12 aa） Fragment：residues 209-220 (Uniprot numbering)
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 MG MAGNESIUM ION × 6 WQN 1-[8-(4-bromophenyl)sulfonyl-5-oxa-2,8-diazaspiro[3.5]nonan-2-yl]-2-chloranyl-ethanone × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；PEG4000, HEPES, CaCl2, glycerol
Resolution 1.50 Å R-free 0.213
8VSN Ternary structure of 14-3-3 sigma, ARAF phosphopeptide (pS214) and compound 79 (1124379) Deposited 2024-01-24 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 × 4 PDB declaration: tetrameric
Chain P 209–220（12 aa） Fragment：residues 209-220 (Uniprot numbering)
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 2 MG MAGNESIUM ION × 6 WQT 2-chloranyl-1-[8-(4-iodophenyl)sulfonyl-5-oxa-2,8-diazaspiro[3.5]nonan-2-yl]ethanone × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；PEG4000, HEPES, CaCl2, glycerol
Resolution 1.91 Å R-free 0.272
9AXM Crystal structure of ARAF/MEK1 complex with NST-628 and a RAF dimer Deposited 2024-03-06 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 × 4 PDB declaration: tetrameric
Chain B 298–576（279 aa）
Chain D 298–576（279 aa）
Mutation：Y301D Y302D Mutation：Y301D Y302D A1AHE N-[3-fluoro-4-({7-[(3-fluoropyridin-2-yl)oxy]-4-methyl-2-oxo-2H-1-benzopyran-3-yl}methyl)pyridin-2-yl]-N'-methylsulfuric diamide × 2 MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；0.1M tri-sodium citrate pH 5.6, 20% 2-propanol, 20% PEG 4000
Resolution 2.42 Å R-free 0.301

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

View Construct and Data Evidence
UniProt name ARAF_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–80； UniProt 19–91

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 1wxm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1wxm
Deposition date deposition_date2005-01-26
Structure title titleSolution Structure of the N-terminal Ras-binding Domain (RBD) in Human a-Raf Kinase
Keywords keywords;Ras-binding domain (RBD), ubiquitin-like fold, a-Raf kinase, Structural genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Transferase ;; TRANSFERASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.51 Å
Radius of gyration Rg (electron density) rg_electron12.70 Å
Forward intensity I(0) i0474020000.00
Molecular weight molecular_weight181990.0 kDa
Excluded volume excluded_volume227790 ų
Envelope volume envelope_volume30152 ų
Hydration-shell volume shell_volume15105 ų
Envelope diameter envelope_diameter64.4 Å
Shell Rg shell_rg23.09 Å
Envelope Rg envelope_rg17.89 Å
Shape Rg shape_rg12.67 Å
Total Rg total_rg13.09 Å
Total atoms total_atoms25860
Residues n_residues1720
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 dmax35.1 Å
Rg (real space) rg_real12.82 Å
Rg uncertainty (real space) rg_real_error0.04 Å
I(0) (real space) i0_real4.5310e+08
I(0) uncertainty (real space) i0_real_error3.1860e+06
Rg (reciprocal space) rg_reciprocal13.52 Å
I(0) (reciprocal space) i0_reciprocal474000000.0000
Solution quality estimate total_estimate0.6813
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks0
Primary peak position r_peak_primary— Å
Skewness Skewness skewness0.100
Kurtosis Kurtosis kurtosis-0.353
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha3.9720
Highest regularization parameter α highest_alpha147900.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.003; Oscil: 0.986; Stabil: 0.972; Sysdev: 0.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1wxma1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.5 — Ras-binding domain, RBD
Domain ID domain_idd1wxma2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1wxma3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id1wxmA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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8. Citations (1)

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9. Files and Curves (10)