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1r4m

APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex

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

amyloid beta precursor protein-binding protein 1

Homo sapiens

UniProt Q13564

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 ubiquitin-activating enzyme E1C × 1 （Q8TBC4） Ubiquitin-like protein NEDD8 × 1 （Q15843） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 ubiquitin-activating enzyme E1C × 1 （Q8TBC4） Ubiquitin-like protein NEDD8 × 1 （Q15843） ZINC ION × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 ubiquitin-activating enzyme E1C × 1 （Q8TBC4） Ubiquitin-like protein NEDD8 × 1 （Q15843） ZINC ION × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 ubiquitin-activating enzyme E1C × 1 （Q8TBC4） Ubiquitin-like protein NEDD8 × 1 （Q15843） ZINC ION × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1r4m 1r4m 1r4m 1r4m 1r4n 1r4n 1r4n 1r4n 1yov 1yov 2nvu 3dbh

25 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name ULA1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–529； UniProt 1–534 Author chain C； PDBConstruct 1–529； UniProt 1–534 Author chain E； PDBConstruct 1–529； UniProt 1–534 Author chain G； PDBConstruct 1–529； UniProt 1–534

ubiquitin-activating enzyme E1C

Homo sapiens

UniProt Q8TBC4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 amyloid beta precursor protein-binding protein 1 × 1 （Q13564） Ubiquitin-like protein NEDD8 × 1 （Q15843） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 amyloid beta precursor protein-binding protein 1 × 1 （Q13564） Ubiquitin-like protein NEDD8 × 1 （Q15843） ZINC ION × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 amyloid beta precursor protein-binding protein 1 × 1 （Q13564） Ubiquitin-like protein NEDD8 × 1 （Q15843） ZINC ION × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 amyloid beta precursor protein-binding protein 1 × 1 （Q13564） Ubiquitin-like protein NEDD8 × 1 （Q15843） ZINC ION × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2lq7

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1r4m 1r4m 1r4m 1r4m 1r4n 1r4n 1r4n 1r4n 1y8x 1yov 1yov 2nvu

27 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBA3_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–431； UniProt 33–463 Author chain D； PDBConstruct 1–431； UniProt 33–463 Author chain F； PDBConstruct 1–431； UniProt 33–463 Author chain H； PDBConstruct 1–431； UniProt 33–463

Ubiquitin-like protein NEDD8

Homo sapiens

UniProt Q15843

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 amyloid beta precursor protein-binding protein 1 × 1 （Q13564） ubiquitin-activating enzyme E1C × 1 （Q8TBC4） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 amyloid beta precursor protein-binding protein 1 × 1 （Q13564） ubiquitin-activating enzyme E1C × 1 （Q8TBC4） ZINC ION × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 amyloid beta precursor protein-binding protein 1 × 1 （Q13564） ubiquitin-activating enzyme E1C × 1 （Q8TBC4） ZINC ION × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 amyloid beta precursor protein-binding protein 1 × 1 （Q13564） ubiquitin-activating enzyme E1C × 1 （Q8TBC4） ZINC ION × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1ndd 1ndd 1ndd 1ndd 2ko3

5 assemblies

Homodimer

None

Homotetramer
1ndd

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
1r4m 1r4m 1r4m 1r4m 1r4n 1r4n 1r4n 1r4n 1xt9 2bkr 2n7k 2nvu

66 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NEDD8_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain I； PDBConstruct 1–76； UniProt 1–76 Author chain J； PDBConstruct 1–76； UniProt 1–76 Author chain K； PDBConstruct 1–76； UniProt 1–76 Author chain L； 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_id1r4m
Deposition date deposition_date2003-10-07
Structure title titleAPPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex
Keywords keywordsCELL CYCLE; CELL CYCLE
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.

1r4m__assembly_1__model_1

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

Download this curve (.dat)

1r4m__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.

1r4m__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）31.25 Å
Rg (electron density)29.99 Å
Total Rg30.69 Å
Atom count7904
Residues1010
Excluded volume140670 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1r4m__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1r4m__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1r4m__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1r4m__assembly_4__model_1 trimeric （3） 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) 32 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1r4ma_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd1r4mb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd1r4mc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd1r4md_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd1r4me_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd1r4mf_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd1r4mg_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd1r4mh_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.111 — Activating enzymes of the ubiquitin-like proteins
Superfamily Superfamily superfamilyc.111.1 — Activating enzymes of the ubiquitin-like proteins
Family Family familyc.111.1.2 — Ubiquitin activating enzymes (UBA)
Domain ID domain_idd1r4mi_
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_idd1r4mj_
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_idd1r4mk_
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_idd1r4ml_
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 (20 domains)

Domain ID domain_id1r4mA01
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_id1r4mB01
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_id1r4mB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily520 — Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
Domain ID domain_id1r4mB03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily260 — NEDD8-activating enzyme E1, catalytic subunit
Domain ID domain_id1r4mC01
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_id1r4mD01
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_id1r4mD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily520 — Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
Domain ID domain_id1r4mD03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily260 — NEDD8-activating enzyme E1, catalytic subunit
Domain ID domain_id1r4mE01
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_id1r4mF01
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_id1r4mF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily520 — Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
Domain ID domain_id1r4mF03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily260 — NEDD8-activating enzyme E1, catalytic subunit
Domain ID domain_id1r4mG01
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_id1r4mH01
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_id1r4mH02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily520 — Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
Domain ID domain_id1r4mH03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily260 — NEDD8-activating enzyme E1, catalytic subunit
Domain ID domain_id1r4mI00
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_id1r4mJ00
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_id1r4mK00
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_id1r4mL00
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)