← Back to search
5nbl

Crystal structure of the Arp4-N-actin(APO-state) heterodimer bound by a nanobody

Method: X-RAY DIFFRACTION
▼

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

Actin-related protein 4

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P80428

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Actin × 1 （P60010） nAct-Nanobody × 1 Unknown peptide × 1 CALCIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Actin × 1 （P60010） nAct-Nanobody × 1 Unknown peptide × 1 CALCIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3qb0 3qb0 3qb0 3qb0

4 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5i9e 5i9e 5nbl 5nbl 5nbm 5nbm 5nbn 5nbn 5y81 7vvy 7vvz 8a5a

14 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ARP4_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–489； UniProt 1–489 Author chain B； PDBConstruct 1–489； UniProt 1–489

Actin

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P60010

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Actin-related protein 4 × 1 （P80428） nAct-Nanobody × 1 Unknown peptide × 1 CALCIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Actin-related protein 4 × 1 （P80428） nAct-Nanobody × 1 Unknown peptide × 1 CALCIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers
9go5

1 assemblies

Heteromeric or nucleic-acid complex
1yag 1yag 1yvn 1yvn 5nbl 5nbl 5nbm 5nbm 5nbn 5nbn 5y81 7vvy

18 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ACT_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–375； UniProt 1–375 Author chain D； PDBConstruct 1–375； UniProt 1–375

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_id5nbl
Deposition date deposition_date2017-03-02
Structure title titleCrystal structure of the Arp4-N-actin(APO-state) heterodimer bound by a nanobody
Keywords keywordsNuclear actin, Actin-related-proteins, Chromatin remodeling, Nanobody, INO80, SWR1, NuA4, hydrolase; HYDROLASE
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.

5nbl__assembly_1__model_1

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

Download this curve (.dat)

5nbl__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5nbl__assembly_1__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）30.29 Å
Rg (electron density)29.39 Å
Total Rg30.11 Å
Atom count7057
Residues906
Excluded volume124970 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5nbl__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5nbl__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

▼

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd5nblc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.1 — Actin/HSP70
Domain ID domain_idd5nblc2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.1 — Actin/HSP70
Domain ID domain_idd5nbld1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.1 — Actin/HSP70
Domain ID domain_idd5nbld2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.1 — Actin/HSP70
Domain ID domain_idd5nble_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd5nblf_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (12 domains)

Domain ID domain_id5nblA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id5nblA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id5nblA03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily10 — ATPase, substrate binding domain, subdomain 4
Domain ID domain_id5nblB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id5nblB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id5nblB03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily10 — ATPase, substrate binding domain, subdomain 4
Domain ID domain_id5nblC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id5nblC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id5nblC03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily10 — ATPase, substrate binding domain, subdomain 4
Domain ID domain_id5nblD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id5nblD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id5nblD03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily10 — ATPase, substrate binding domain, subdomain 4
▶

7. Citations (1)