← Back to search
3wa0

Crystal structure of merlin complexed with DCAF1/VprBP

Method: X-RAY DIFFRACTION
▼

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

Merlin

Mus musculus

UniProt P46662

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Protein VPRBP × 1 （Q9Y4B6） water × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Protein VPRBP × 1 （Q9Y4B6） water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Protein VPRBP × 1 water × 1 Consistent with protein count
4 Protein monomer Monomer Protein 1 water × 1 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 2 Protein VPRBP × 1 water × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 2 Protein VPRBP × 1 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1isn 3wa0

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3wa0 3wa0 3wa0 3wa0 3wa0 4p7i 4p7i 4zrk 4zrk 4zrk 4zrk

11 assemblies

View Construct and Data Evidence
UniProt name MERL_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–301； UniProt 19–314 Author chain B； PDBConstruct 6–301； UniProt 19–314 Author chain C； PDBConstruct 6–301； UniProt 19–314 Author chain D； PDBConstruct 6–301； UniProt 19–314 Author chain E； PDBConstruct 6–301； UniProt 19–314 Author chain F； PDBConstruct 6–301； UniProt 19–314

Protein VPRBP

Homo sapiens

UniProt Q9Y4B6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Merlin × 1 （P46662） water × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Merlin × 1 （P46662） water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
4pxw 4pxw 7ufv 7ufv 8f8e 8f8e 8og5 8og6 8og7 8og8 8og9 8oga

31 assemblies; showing the first 12

Homodimer
7sse 9ply 9y4q

3 assemblies

Homotetramer

None

Other homooligomers
9zl9 9zle 9zlg 9zli

4 assemblies

Heteromeric or nucleic-acid complex
3wa0 3wa0 4cc9 4p7i 4p7i 4z8l 4z8l 5aja 5jk7 5jk7 6n45 6zue

23 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name VPRBP_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain G； PDBConstruct 7–96； UniProt 1417–1506 Author chain H； PDBConstruct 7–96； UniProt 1417–1506

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id3wa0
Deposition date deposition_date2013-04-20
Structure title titleCrystal structure of merlin complexed with DCAF1/VprBP
Keywords keywordsmerlin FERM domain, CELL ADHESION; CELL ADHESION
Experimental Method methodX-RAY DIFFRACTION
▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3wa0__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3wa0__assembly_2__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3wa0__assembly_2__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）22.60 Å
Rg (electron density)21.50 Å
Total Rg22.53 Å
Atom count2488
Residues301
Excluded volume44741 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3wa0__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3wa0__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3wa0__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3wa0__assembly_4__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 3wa0__assembly_5__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 3wa0__assembly_6__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

▼

6. Fold Classification (SCOP + CATH) 36 domains

SCOP 2.08 (18 domains)

Domain ID domain_idd3wa0a1
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.15.1.0 — automated matches
Domain ID domain_idd3wa0a2
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.0 — automated matches
Domain ID domain_idd3wa0a3
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches
Domain ID domain_idd3wa0b1
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.15.1.0 — automated matches
Domain ID domain_idd3wa0b2
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.0 — automated matches
Domain ID domain_idd3wa0b3
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches
Domain ID domain_idd3wa0c1
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.15.1.0 — automated matches
Domain ID domain_idd3wa0c2
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.0 — automated matches
Domain ID domain_idd3wa0c3
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches
Domain ID domain_idd3wa0d1
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.15.1.0 — automated matches
Domain ID domain_idd3wa0d2
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.0 — automated matches
Domain ID domain_idd3wa0d3
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches
Domain ID domain_idd3wa0e1
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.15.1.0 — automated matches
Domain ID domain_idd3wa0e2
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.0 — automated matches
Domain ID domain_idd3wa0e3
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches
Domain ID domain_idd3wa0f1
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.15.1.0 — automated matches
Domain ID domain_idd3wa0f2
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.0 — automated matches
Domain ID domain_idd3wa0f3
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches

CATH v4.4 (18 domains)

Domain ID domain_id3wa0A01
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
Domain ID domain_id3wa0A02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3wa0A03
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_id3wa0B01
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
Domain ID domain_id3wa0B02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3wa0B03
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_id3wa0C01
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
Domain ID domain_id3wa0C02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3wa0C03
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_id3wa0D01
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
Domain ID domain_id3wa0D02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3wa0D03
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_id3wa0E01
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
Domain ID domain_id3wa0E02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3wa0E03
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_id3wa0F01
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
Domain ID domain_id3wa0F02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10 —
Domain ID domain_id3wa0F03
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)
▶

7. Citations (1)