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3umi

X-ray structure of the E2 domain of the human amyloid precursor protein (APP) in complex with zinc

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

Amyloid beta A4 protein

Homo sapiens

UniProt P05067

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein monomer Monomer Protein 1 ACETATE ION × 1 ZINC ION × 1 CADMIUM ION × 8 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1amb 1amc 1aml 1ba4 1ba6 1bjb 1bjc 1hz3 1iyt 1mwp 1owt 1qcm

64 assemblies; showing the first 12

Homodimer
1aap 2loh 2lz3 2lz4 2mgt 2y3k 2y3k 2y3k 2y3k 3ktm 3ktm 3ktm

18 assemblies; showing the first 12

Homotetramer
2y3j 2y3j 2y3l 3ovj 6rhy 6wxm 6wxm

7 assemblies

Other homooligomers
11en 11eo 11ep 12gb 21fb 2beg 2lmn 2lmo 2lmp 2lmq 2lnq 2m4j

99 assemblies; showing the first 12

Heteromeric or nucleic-acid complex
1brc 1ca0 1ca0 1taw 1x11 1x11 1x11 1zjd 2otk 2r0w 2wk3 2wk3

95 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name A4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–207； UniProt 370–575

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_id3umi
Deposition date deposition_date2011-11-13
Structure title titleX-ray structure of the E2 domain of the human amyloid precursor protein (APP) in complex with zinc
Keywords keywordsmetal binding site, metal binding, cell surface, secretory pathway, metal binding protein; METAL BINDING PROTEIN
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.

3umi__assembly_1__model_1

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

Download this curve (.dat)

3umi__assembly_1__model_1 | I(q)

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

3umi__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）25.25 Å
Rg (electron density)26.08 Å
Total Rg26.04 Å
Atom count1547
Residues183
Excluded volume27465 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3umi__assembly_1__model_1 monomeric （1） 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 (5)

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3umia_
Class classa — All alpha proteins
Fold Fold folda.47 — STAT-like
Superfamily Superfamily superfamilya.47.4 — CAPPD, an extracellular domain of amyloid beta A4 protein
Family Family familya.47.4.1 — CAPPD, an extracellular domain of amyloid beta A4 protein

CATH v4.4 (1 domains)

Domain ID domain_id3umiA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily770 — Amyloid precursor protein, E2 domain
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7. Citations (1)