2uzx

Structure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein InlB: Crystal form I

Method: X-RAY DIFFRACTION Dmax: 132.4 Å Quality: GOOD

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

INTERNALIN B

LISTERIA MONOCYTOGENES

UniProt P25147

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 36–321 Fragment:INTERNALIN DOMAIN (CAP, LRR, IR), INLB321, RESIDUES 36-320 HEPATOCYTE GROWTH FACTOR RECEPTOR × 1 (P08581) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;20 DEG C VAPOR DIFFUSION. 2 UL PROTEIN (5 MG/ML) PLUS 1 UL RESERVOIR CONSISTING OF 16.5% PEG 1500, 4.4% MPD, 0.1 M TRIS, PH8.5. RESERVOIR WAS COVERED WITH ALS OIL. Resolution 2.80 Å R-free 0.307
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 36–321 Fragment:INTERNALIN DOMAIN (CAP, LRR, IR), INLB321, RESIDUES 36-320 HEPATOCYTE GROWTH FACTOR RECEPTOR × 1 (P08581) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;20 DEG C VAPOR DIFFUSION. 2 UL PROTEIN (5 MG/ML) PLUS 1 UL RESERVOIR CONSISTING OF 16.5% PEG 1500, 4.4% MPD, 0.1 M TRIS, PH8.5. RESERVOIR WAS COVERED WITH ALS OIL. Resolution 2.80 Å R-free 0.307

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.

16 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INLB_LISMO
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–289; UniProt 36–321 Author chain C; PDBConstruct 4–289; UniProt 36–321

HEPATOCYTE GROWTH FACTOR RECEPTOR

HOMO SAPIENS

UniProt P08581

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 25–740 Fragment:SEMA, PSI, IG1, MET741, RESIDUES 25-740 INTERNALIN B × 1 (P25147) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;20 DEG C VAPOR DIFFUSION. 2 UL PROTEIN (5 MG/ML) PLUS 1 UL RESERVOIR CONSISTING OF 16.5% PEG 1500, 4.4% MPD, 0.1 M TRIS, PH8.5. RESERVOIR WAS COVERED WITH ALS OIL. Resolution 2.80 Å R-free 0.307
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 25–740 Fragment:SEMA, PSI, IG1, MET741, RESIDUES 25-740 INTERNALIN B × 1 (P25147) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;293 K;20 DEG C VAPOR DIFFUSION. 2 UL PROTEIN (5 MG/ML) PLUS 1 UL RESERVOIR CONSISTING OF 16.5% PEG 1500, 4.4% MPD, 0.1 M TRIS, PH8.5. RESERVOIR WAS COVERED WITH ALS OIL. Resolution 2.80 Å R-free 0.307

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.

128 other PDB entries and 165 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MET_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 4–719; UniProt 25–740 Author chain D; PDBConstruct 4–719; UniProt 25–740

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 2uzx

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2uzx
Deposition date deposition_date2007-05-02
Structure title titleStructure of the human receptor tyrosine kinase Met in complex with the Listeria monocytogenes invasion protein InlB: Crystal form I
Keywords keywords;SIGNALING PROTEIN/RECEPTOR, LEUCINE RICH REPEAT, RECEPTOR ECTODOMAIN, HEPATOCYTE GROWTH FACTOR RECEPTOR, SIGNALING PROTEIN, ATP-BINDING, TRANSFERASE, POLYMORPHISM, GLYCOPROTEIN, VIRULENCE FACTOR, DISEASE MUTATION, NUCLEOTIDE-BINDING, TRANSMEMBRANE, PROTO-ONCOGENE, PHOSPHORYLATION, LEUCINE-RICH REPEAT, ALTERNATIVE SPLICING, TYROSINE-PROTEIN KINASE, CHROMOSOMAL REARRANGEMENT, LRR, HGFR, KINASE, MEMBRANE, RECEPTOR, INTERNALIN, SIGNALING PROTEIN-RECEPTOR COMPLEX ;; SIGNALING PROTEIN/RECEPTOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier39.52
Radius of gyration Rg (electron density) rg_electron39.05
Forward intensity I(0) i0511125000.00
Molecular weight molecular_weight187090.0 kDa
Excluded volume excluded_volume235350 ų
Envelope volume envelope_volume312340 ų
Hydration-shell volume shell_volume66130 ų
Envelope diameter envelope_diameter143.1
Shell Rg shell_rg45.33
Envelope Rg envelope_rg38.49
Shape Rg shape_rg39.06
Total Rg total_rg39.35
Total atoms total_atoms13170
Residues n_residues1668
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 dmax132.4
Rg (real space) rg_real39.48
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real5.1110e+08
I(0) uncertainty (real space) i0_real_error9.1290e+06
Rg (reciprocal space) rg_reciprocal39.51
I(0) (reciprocal space) i0_reciprocal511100000.0000
Solution quality estimate total_estimate0.8728
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.4
Skewness Skewness skewness0.364
Kurtosis Kurtosis kurtosis-0.237
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha90220000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.839

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd2uzxa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamilyc.10.2 — L domain-like
Family Family familyc.10.2.1 — Internalin LRR domain
Domain ID domain_idd2uzxa2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.0 — automated matches
Domain ID domain_idd2uzxa3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2uzxc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamilyc.10.2 — L domain-like
Family Family familyc.10.2.1 — Internalin LRR domain
Domain ID domain_idd2uzxc2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.0 — automated matches
Domain ID domain_idd2uzxc3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id2uzxA01
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id2uzxA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1220
Domain ID domain_id2uzxB01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id2uzxB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2uzxC01
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id2uzxC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1220
Domain ID domain_id2uzxD01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id2uzxD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)