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4am7

ADP-BOUND C-TERMINAL DOMAIN OF ACTIN-RELATED PROTEIN ARP8 FROM S. CEREVISIAE

Method: X-RAY DIFFRACTION Dmax: 137.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ACTIN-LIKE PROTEIN ARP8

SACCHAROMYCES CEREVISIAE

UniProt Q12386

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 248–881 Fragment：C-TERMINAL DOMAIN, RESIDUES 248-881 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；19.5% W/V PEG 5000 MME, 0.32 M LI2SO4, 0.1 M MES PH 6.5, 0.002 M ADP, 0.005 M MGCL2 Resolution 3.25 Å R-free 0.284
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 248–881 Fragment：C-TERMINAL DOMAIN, RESIDUES 248-881 ADP ADENOSINE-5'-DIPHOSPHATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；19.5% W/V PEG 5000 MME, 0.32 M LI2SO4, 0.1 M MES PH 6.5, 0.002 M ADP, 0.005 M MGCL2 Resolution 3.25 Å R-free 0.284

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 4AM7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4AM6 C-TERMINAL DOMAIN OF ACTIN-RELATED PROTEIN ARP8 FROM S. CEREVISIAE Deposited 2012-03-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 248–881（634 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 248-881
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；18% W/V PEG 5000 MME, 0.28 M LI2SO4, 0.1 M NA-CACODYLATE PH 6.5
Resolution 2.70 Å R-free 0.286
4AM6 C-TERMINAL DOMAIN OF ACTIN-RELATED PROTEIN ARP8 FROM S. CEREVISIAE Deposited 2012-03-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 248–881（634 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 248-881
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；18% W/V PEG 5000 MME, 0.28 M LI2SO4, 0.1 M NA-CACODYLATE PH 6.5
Resolution 2.70 Å R-free 0.286
5NBN Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80 Deposited 2017-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 255–881（627 aa）
Not recorded CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 LAR LATRUNCULIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium citrate tribasic dihydrate, 18% (w/v) polyethylene glycol 3,350, latrunculin A solved in DMSO molar ration 1:1.5 (protein : latrunculin A)
Resolution 4.00 Å R-free 0.242
5NBN Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80 Deposited 2017-03-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 255–881（627 aa）
Not recorded CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 LAR LATRUNCULIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium citrate tribasic dihydrate, 18% (w/v) polyethylene glycol 3,350, latrunculin A solved in DMSO molar ration 1:1.5 (protein : latrunculin A)
Resolution 4.00 Å R-free 0.242
8A5A Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of INO80 Deposited 2022-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain U 1–881（881 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8A5O Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80 Deposited 2022-06-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain U 1–881（881 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ARP8_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 22–655； UniProt 248–881 Author chain B； PDBConstruct 22–655； UniProt 248–881

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 4am7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4am7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4am7
Deposition date deposition_date2012-03-07
Structure title titleADP-BOUND C-TERMINAL DOMAIN OF ACTIN-RELATED PROTEIN ARP8 FROM S. CEREVISIAE
Keywords keywords;NUCLEAR PROTEIN, CHROMATIN REMODELLING COMPLEX, ATP-BINDING PROTEIN, NUCLEAR ACTIN-RELATED PROTEIN, TRANSCRIPTION REGULATION, DNA REPAIR ;; NUCLEAR PROTEIN
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_guinier40.35 Å
Radius of gyration Rg (electron density) rg_electron40.09 Å
Forward intensity I(0) i0302334000.00
Molecular weight molecular_weight143480.0 kDa
Excluded volume excluded_volume180380 ų
Envelope volume envelope_volume249390 ų
Hydration-shell volume shell_volume53048 ų
Envelope diameter envelope_diameter147.9 Å
Shell Rg shell_rg44.28 Å
Envelope Rg envelope_rg39.79 Å
Shape Rg shape_rg40.09 Å
Total Rg total_rg40.32 Å
Total atoms total_atoms10126
Residues n_residues1246
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 dmax137.7 Å
Rg (real space) rg_real40.49 Å
Rg uncertainty (real space) rg_real_error1.26 Å
I(0) (real space) i0_real3.0230e+08
I(0) uncertainty (real space) i0_real_error4.8090e+06
Rg (reciprocal space) rg_reciprocal40.35 Å
I(0) (reciprocal space) i0_reciprocal302300000.0000
Solution quality estimate total_estimate0.6355
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.8 Å
Skewness Skewness skewness0.433
Kurtosis Kurtosis kurtosis-0.372
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha85150000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 0.025; Positv: 1.000; Valcen: 0.875; Smooth: 0.806
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id4am7A01
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_id4am7A02
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_id4am7A03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily580 —
Domain ID domain_id4am7B01
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_id4am7B02
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_id4am7B03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily580 —
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8. Citations (1)

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9. Files and Curves (10)