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3cmm

Crystal Structure of the Uba1-Ubiquitin Complex

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin-activating enzyme E1 1

Saccharomyces cerevisiae

UniProt P22515

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Ubiquitin × 1 （P61864） PROLINE × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Ubiquitin × 1 （P61864） PROLINE × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
7zh9

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3cmm 3cmm 4nnj 5l6h 5l6h 5l6i 5l6i 5l6j 5l6j 5tr4 5tr4 6nya

29 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBA1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1015； UniProt 10–1024 Author chain C； PDBConstruct 1–1015； UniProt 10–1024

Ubiquitin

Saccharomyces cerevisiae

UniProt P61864

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Ubiquitin-activating enzyme E1 1 × 1 （P22515） PROLINE × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Ubiquitin-activating enzyme E1 1 × 1 （P22515） PROLINE × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1zw7 2jwz

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1otr 1q0w 1wr1 1zgu 2g3q 2jt4 2l00 3cmm 3cmm 3l0w 3l10

11 assemblies

View Construct and Data Evidence
UniProt name UBIQ_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain D； PDBConstruct 1–76； UniProt 1–76

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id3cmm
Deposition date deposition_date2008-03-23
Structure title titleCrystal Structure of the Uba1-Ubiquitin Complex
Keywords keywords;Ubiquitin, E1, Uba1, Protein turnover, ligase, Conformational change, thioester, adenylation, transthioesterification, ATP-binding, Nucleotide-binding, Nucleus, Phosphoprotein, Ubl conjugation pathway, DNA damage, DNA repair, LIGASE-PROTEIN BINDING COMPLEX ;; LIGASE/PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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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.

3cmm__assembly_1__model_1

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

Download this curve (.dat)

3cmm__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.

3cmm__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）33.79 Å
Rg (electron density)32.95 Å
Total Rg33.54 Å
Atom count8519
Residues1077
Excluded volume151980 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3cmm__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3cmm__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3cmmb_
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.15.1.1 — Ubiquitin-related
Domain ID domain_idd3cmmd_
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.15.1.1 — Ubiquitin-related

CATH v4.4 (14 domains)

Domain ID domain_id3cmmA01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily80 — Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1
Domain ID domain_id3cmmA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12550 — Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2
Domain ID domain_id3cmmA03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily180 — Ubiquitin-activating enzyme E1, FCCH domain
Domain ID domain_id3cmmA04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3cmmA05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily2660 — Ubiquitin-activating enzyme E1, SCCH domain
Domain ID domain_id3cmmA06
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily60 — Ubiquitin-activating enzyme E1, UFD domain
Domain ID domain_id3cmmB00
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_id3cmmC01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily80 — Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1
Domain ID domain_id3cmmC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily12550 — Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2
Domain ID domain_id3cmmC03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily180 — Ubiquitin-activating enzyme E1, FCCH domain
Domain ID domain_id3cmmC04
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3cmmC05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily2660 — Ubiquitin-activating enzyme E1, SCCH domain
Domain ID domain_id3cmmC06
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily60 — Ubiquitin-activating enzyme E1, UFD domain
Domain ID domain_id3cmmD00
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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7. Citations (1)