4nge

Crystal Structure of Human Presequence Protease in Complex with Amyloid-beta (1-40)

Method: X-RAY DIFFRACTION

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

Presequence protease, mitochondrial

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Beta-amyloid protein 40 × 1 （P05067） Beta-amyloid protein 40 × 1 ZINC ION × 1 GLYCEROL × 1 ACETATE ION × 2 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Beta-amyloid protein 40 × 1 （P05067） Beta-amyloid protein 40 × 1 ZINC ION × 1 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PREP_HUMAN
Isoform	—
PDB entities	1, 4
Chains and sequence ranges	Author chain A； PDBConstruct 10–1014； UniProt 33–1037 Author chain D； PDBConstruct 10–1014； UniProt 33–1037

Beta-amyloid protein 40

OrganismNot specified

UniProt P05067

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Presequence protease, mitochondrial × 1 （Q5JRX3） Beta-amyloid protein 40 × 1 ZINC ION × 1 GLYCEROL × 1 ACETATE ION × 2 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Beta-amyloid protein 40 × 1 Presequence protease, mitochondrial × 1 （Q5JRX3） ZINC ION × 1 GLYCEROL × 2 water × 2	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–40； UniProt 672–711 Author chain E； PDBConstruct 1–40； UniProt 672–711

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	4nge
Deposition date deposition_date	2013-11-01
Structure title title	Crystal Structure of Human Presequence Protease in Complex with Amyloid-beta (1-40)
Keywords keywords	;M16 metalloprotease, Alzheimer's disease, zinc metalloendoprotease, monomethyllysine, dimethyllysine, S-(dimethylarsenic)cysteine, mitochondrial matrix, HYDROLASE-PROTEIN BINDING complex ;; HYDROLASE/PROTEIN BINDING
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.

4nge__assembly_1__model_1

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

Download this curve (.dat)

4nge__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4nge__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.84 Å
Rg (electron density)	28.69 Å
Total Rg	29.63 Å
Atom count	8008
Residues	977
Excluded volume	143030 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4nge__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4nge__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Description description	Presequence protease, mitochondrial
Molecular weight formula_weight	115762.1 kDa
EC 编号 ec_number	3.4.24.-
Mutation mutation	E107Q
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	16054

MHHHHHHAAACERALQYKLGDKIHGFTVNQVTSVPELFLTAVKLTHDDTGARYLHLAREDTNNLFSVQFRTTPMDSTGVPHILQHTVLCGSQKYPCRDPFFKMLNRSLSTFMNAFTASDYTLYPFSTQNPKDFQNLLSVYLDATFFPCLRELDFWQEGWRLEHENPSDPQTPLVFKGVVFNEMKGAFTDNERIFSQHLQNRLLPDHTYSVVSGGDPLCIPELTWEQLKQFHATHYHPSNARFFTYGNFPLEQHLKQIHEEALSKFQKIEPSTVVPAQTPWDKPREFQITCGPDSFATDPSKQTTVSVSFLLPDITDTFEAFTLSLLSSLLTSGPNSPFYKALIESGLGTDFSPDVGYNGYTREAYFSVGLQGIVEKDIETVRSLIDRTIDEVVEKGFEDDRIEALLHKIEIQMKHQSTSFGLMLTSYIASCWNHDGDPVELLKLGNQLAKFRQCLQENPKFLQEKVKQYFKNNQHKLTLSMRPDDKYHEKQAQVEATKLKQKVEALSPGDRQQIYEKGLELRSQQSKPQDASCLPALKVSDIEPTIPVTELDVVLTAGDIPVQYCAQPTNGMVYFRAFSSLNTLPEELRPYVPLFCSVLTKLGCGLLDYREQAQQIELKTGGMSASPHVLPDDSHMDTYEQGVLFSSLCLDRNLPDMMQLWSEIFNNPCFEEEEHFKVLVKMTAQELANGIPDSGHLYASIRAGRTLTPAGDLQETFSGMDQVRLMKRIAEMTDIKPILRKLPRIKKHLLNGDNMRCSVNATPQQMPQTEKAVEDFLRSIGRSKKERRPVRPHTVEKPVPSSSGGDAHVPHGSQVIRKLVMEPTFKPWQMKTHFLMPFPVNYVGECIRTVPYTDPDHASLKILARLMTAKFLHTEIREKGGAYGGGAKLSHNGIFTLYSYRDPNTIETLQSFGKAVDWAKSGKFTQQDIDEAKLSVFSTVDAPVAPSDKGMDHFLYGLSDEMKQAHREQLFAVSHDKLLAVSDRYLGTGKSTHGLAILGPENPKIAKDPSWIIR

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 polymer

Description description	Beta-amyloid protein 40
Molecular weight formula_weight	4335.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV

Entity 3 Entity 3 polymer

Description description	Beta-amyloid protein 40
Molecular weight formula_weight	613.7 kDa
EC 编号 ec_number	3.4.24.-
Mutation mutation	E107Q
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

XXXXXXX

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 4 Entity 4 polymer

Description description	Presequence protease, mitochondrial
Molecular weight formula_weight	115572.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	40

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	4ngeA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	4ngeA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	4ngeA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	4ngeA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	4ngeD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	4ngeD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	4ngeD03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

Domain ID domain_id	4ngeD04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

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Unit-cell length a length_a	247.275 Å
Unit-cell length b length_b	86.183 Å
Unit-cell length c length_c	158.611 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	127.56 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.704 Å
Low-resolution limit resolution_low	39.621 Å
R factor r_factor	0.1930
R_work r_work	0.1908
R_free r_free	0.2323

Crystal Structure of Human Presequence Protease in Complex with Amyloid-beta (1-40)

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

Presequence protease, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Beta-amyloid protein 40

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

4nge__assembly_1__model_1

4nge__assembly_1__model_1 | I(q)

4nge__assembly_1__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of Human Presequence Protease in Complex with Amyloid-beta (1-40)

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

Presequence protease, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beta-amyloid protein 40

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

4nge__assembly_1__model_1

4nge__assembly_1__model_1 | I(q)

4nge__assembly_1__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)