3ktm

Structure of the Heparin-induced E1-Dimer of the Amyloid Precursor Protein (APP)

Method: X-RAY DIFFRACTION

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

Amyloid beta A4 protein

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	(3R)-butane-1,3-diol × 2 SULFATE ION × 1 ACETATE ION × 1 water × 2	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	(3R)-butane-1,3-diol × 1 water × 1	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	(3R)-butane-1,3-diol × 1 water × 1	Consistent with protein count
12	Protein monomer	Monomer	Protein 1	(3R)-butane-1,3-diol × 1 SULFATE ION × 1 ACETATE ION × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	(3R)-butane-1,3-diol × 2 SULFATE ION × 2 ACETATE ION × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	(3R)-butane-1,3-diol × 2 SULFATE ION × 1 ACETATE ION × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	(3R)-butane-1,3-diol × 2 SULFATE ION × 1 ACETATE ION × 1 water × 2	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	(3R)-butane-1,3-diol × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	(3R)-butane-1,3-diol × 1 SULFATE ION × 1 ACETATE ION × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	(3R)-butane-1,3-diol × 1 SULFATE ION × 1 ACETATE ION × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	(3R)-butane-1,3-diol × 1 SULFATE ION × 1 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	(3R)-butane-1,3-diol × 1 SULFATE ION × 1 ACETATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–174； UniProt 18–190 Author chain B； PDBConstruct 2–174； UniProt 18–190 Author chain C； PDBConstruct 2–174； UniProt 18–190 Author chain D； PDBConstruct 2–174； UniProt 18–190 Author chain E； PDBConstruct 2–174； UniProt 18–190 Author chain F； PDBConstruct 2–174； UniProt 18–190 Author chain G； PDBConstruct 2–174； UniProt 18–190 Author chain H； PDBConstruct 2–174； UniProt 18–190

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_id	3ktm
Deposition date deposition_date	2009-11-25
Structure title title	Structure of the Heparin-induced E1-Dimer of the Amyloid Precursor Protein (APP)
Keywords keywords	;Protein Structure, Alzheimer disease, Amyloid, Amyloidosis, Apoptosis, Cell adhesion, Copper, Disease mutation, Disulfide bond, Endocytosis, Heparin-binding, Metal-binding, Neurodegeneration, Notch signaling pathway, Proteoglycan, Zinc, SIGNALING PROTEIN ;; CELL ADHESION, SIGNALING PROTEIN
Experimental Method method	X-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.

3ktm__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3ktm__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ktm__assembly_5__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	19.15 Å
Rg (electron density)	18.19 Å
Total Rg	19.30 Å
Atom count	1398
Residues	175
Excluded volume	24908 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ktm__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ktm__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3ktm__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3ktm__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3ktm__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3ktm__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3ktm__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3ktm__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3ktm__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`3ktm__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`3ktm__assembly_11__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`3ktm__assembly_12__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)

Entity 1 Entity 1 polymer

Description description	Amyloid beta A4 protein
Molecular weight formula_weight	21762.1 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	11436

MLEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKFLHQERMDVCETHLHWHTVAKETCSEKSTNLHDYGMLLPCGIDKFRGVEFVCCPLAIEGRKLAAALEHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	(3R)-butane-1,3-diol
Molecular weight formula_weight	90.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	282

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	3ktmA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	570 — Sugar Binding Protein, Amyloid A4 Protein; Chain A
Homologous superfamily homologous superfamily	10 — Amyloidogenic glycoprotein, heparin-binding domain

Domain ID domain_id	3ktmA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

Domain ID domain_id	3ktmB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	570 — Sugar Binding Protein, Amyloid A4 Protein; Chain A
Homologous superfamily homologous superfamily	10 — Amyloidogenic glycoprotein, heparin-binding domain

Domain ID domain_id	3ktmB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

Domain ID domain_id	3ktmC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	570 — Sugar Binding Protein, Amyloid A4 Protein; Chain A
Homologous superfamily homologous superfamily	10 — Amyloidogenic glycoprotein, heparin-binding domain

Domain ID domain_id	3ktmC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

Domain ID domain_id	3ktmD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	570 — Sugar Binding Protein, Amyloid A4 Protein; Chain A
Homologous superfamily homologous superfamily	10 — Amyloidogenic glycoprotein, heparin-binding domain

Domain ID domain_id	3ktmD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

Domain ID domain_id	3ktmE01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	570 — Sugar Binding Protein, Amyloid A4 Protein; Chain A
Homologous superfamily homologous superfamily	10 — Amyloidogenic glycoprotein, heparin-binding domain

Domain ID domain_id	3ktmE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

Domain ID domain_id	3ktmF01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	570 — Sugar Binding Protein, Amyloid A4 Protein; Chain A
Homologous superfamily homologous superfamily	10 — Amyloidogenic glycoprotein, heparin-binding domain

Domain ID domain_id	3ktmF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

Domain ID domain_id	3ktmG01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	570 — Sugar Binding Protein, Amyloid A4 Protein; Chain A
Homologous superfamily homologous superfamily	10 — Amyloidogenic glycoprotein, heparin-binding domain

Domain ID domain_id	3ktmG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

Domain ID domain_id	3ktmH01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	570 — Sugar Binding Protein, Amyloid A4 Protein; Chain A
Homologous superfamily homologous superfamily	10 — Amyloidogenic glycoprotein, heparin-binding domain

Domain ID domain_id	3ktmH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	140 — Amyloidogenic glycoprotein, copper-binding domain

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Unit-cell length a length_a	143.990 Å
Unit-cell length b length_b	143.990 Å
Unit-cell length c length_c	351.190 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	72

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	29.000 Å
R factor r_factor	—
R_work r_work	0.2151
R_free r_free	0.2499

Structure of the Heparin-induced E1-Dimer of the Amyloid Precursor Protein (APP)

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

Amyloid beta A4 protein

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ktm__assembly_5__model_1

3ktm__assembly_5__model_1 | I(q)

3ktm__assembly_5__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Structure of the Heparin-induced E1-Dimer of the Amyloid Precursor Protein (APP)

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

Amyloid beta A4 protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ktm__assembly_5__model_1

3ktm__assembly_5__model_1 | I(q)

3ktm__assembly_5__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)