SAXSdb — 6xos

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 33–1037	Fragment：UNP residues 33-1037	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.7；20 mM Tris, pH 7.7, 150 mM NaCl, 10mM KCl, 20 mM EDTA and 1 mM 2-mercaptoethanol cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.70 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6XOS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4L3T Crystal Structure of Substrate-free Human Presequence Protease Deposited 2013-06-06	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–1037（1005 aa） Fragment：UNP residues 33-1037	Mutation：E107Q Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 GOL GLYCEROL × 3 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15.2% w/v PEG8000, 15 mM TCEP, 80 mM sodium cacodylate, pH 6.5, 160 mM calcium acetate, 20% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 2.03 Å R-free 0.210
4L3T Crystal Structure of Substrate-free Human Presequence Protease Deposited 2013-06-06	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 33–1037（1005 aa） Fragment：UNP residues 33-1037	Mutation：E107Q Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 GOL GLYCEROL × 4 ACT ACETATE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15.2% w/v PEG8000, 15 mM TCEP, 80 mM sodium cacodylate, pH 6.5, 160 mM calcium acetate, 20% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 2.03 Å R-free 0.210
4NGE Crystal Structure of Human Presequence Protease in Complex with Amyloid-beta (1-40) Deposited 2013-11-01	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 33–1037（1005 aa） Fragment：UNP residues 33-1037	Mutation：E107Q Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 GOL GLYCEROL × 1 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15.2% w/v PEG8000, 15 mM TCEP, 80 mM sodium cacodylate, pH 6.5, 160 mM calcium acetate, 20% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 2.70 Å R-free 0.232
4NGE Crystal Structure of Human Presequence Protease in Complex with Amyloid-beta (1-40) Deposited 2013-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 33–1037（1005 aa） Fragment：SEE REMARK 999	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291.15 K；15.2% w/v PEG8000, 15 mM TCEP, 80 mM sodium cacodylate, pH 6.5, 160 mM calcium acetate, 20% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 2.70 Å R-free 0.232
4RPU Crystal Structure of Human Presequence Protease in Complex with Inhibitor MitoBloCK-60 Deposited 2014-10-31	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–1037（1005 aa） Fragment：UNP residues 33-1037	Mutation：E107Q Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 3UE [4-(diphenylmethyl)piperazin-1-yl](3-methyl-4-nitrophenyl)methanone × 2 GOL GLYCEROL × 11 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；291 K；15.0% PEG 8000, 15 mM TCEP, 80 mM sodium cacodylate pH 6.7, 160 mM calcium acetate, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.27 Å R-free 0.208
4RPU Crystal Structure of Human Presequence Protease in Complex with Inhibitor MitoBloCK-60 Deposited 2014-10-31	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 33–1037（1005 aa） Fragment：UNP residues 33-1037	Mutation：E107Q Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 3UE [4-(diphenylmethyl)piperazin-1-yl](3-methyl-4-nitrophenyl)methanone × 2 GOL GLYCEROL × 7 ACT ACETATE ION × 5 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；291 K；15.0% PEG 8000, 15 mM TCEP, 80 mM sodium cacodylate pH 6.7, 160 mM calcium acetate, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.27 Å R-free 0.208
6XOT CryoEM structure of human presequence protease in partial open state 2 Deposited 2020-07-07	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–1037（1005 aa） Fragment：UNP residues 33-1037	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.7；20 mM Tris, pH 7.7, 150 mM NaCl, 10mM KCl, 20 mM EDTA and 1 mM 2-mercaptoethanol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6XOU CryoEM structure of human presequence protease in open state Deposited 2020-07-07	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–1037（1005 aa） Fragment：UNP residues 33-1037	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.7；20 mM Tris, pH 7.7, 150 mM NaCl, 10mM KCl, 20 mM EDTA and 1 mM 2-mercaptoethanol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
6XOV CryoEM structure of human presequence protease in partial closed state 1 Deposited 2020-07-07	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 33–1037（1005 aa） Fragment：UNP residues 33-1037	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.7；20 mM Tris, pH 7.7, 150 mM NaCl, 10mM KCl, 20 mM EDTA and 1 mM 2-mercaptoethanol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
6XOW CryoEM structure of human presequence protease in partial close state 2, induced by presequence of citrate synthase Deposited 2020-07-07	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–1037（1005 aa） Fragment：UNP residues 33-1037	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.7；20 mM Tris, pH 7.7, 150 mM NaCl, 10mM KCl, 20 mM EDTA and 1 mM 2-mercaptoethanol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å

7 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

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

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	6xos
Deposition date deposition_date	2020-07-07
Structure title title	CryoEM structure of human presequence protease in partial open state 1
Keywords keywords	Partial open state, HYDROLASE; HYDROLASE
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.31 Å
Radius of gyration Rg (electron density) rg_electron	29.12 Å
Forward intensity I(0) i0	189793000.00
Molecular weight molecular_weight	109290.0 kDa
Excluded volume excluded_volume	136920 Å³
Envelope volume envelope_volume	177750 Å³
Hydration-shell volume shell_volume	48929 Å³
Envelope diameter envelope_diameter	93.2 Å
Shell Rg shell_rg	38.10 Å
Envelope Rg envelope_rg	28.28 Å
Shape Rg shape_rg	29.11 Å
Total Rg total_rg	30.03 Å
Total atoms total_atoms	7698
Residues n_residues	966
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	86.4 Å
Rg (real space) rg_real	30.03 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	1.8980e+08
I(0) uncertainty (real space) i0_real_error	2.0450e+06
Rg (reciprocal space) rg_reciprocal	30.15 Å
I(0) (reciprocal space) i0_reciprocal	189800000.0000
Solution quality estimate total_estimate	0.9025
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.5 Å
Skewness Skewness skewness	-0.044
Kurtosis Kurtosis kurtosis	-0.543
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	52370000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.927

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Description description	Presequence protease, mitochondrial
Molecular weight formula_weight	114901.5 kDa
EC 编号 ec_number	3.4.24.-
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	7704

MHHHHHHAAACERALQYKLGDKIHGFTVNQVTSVPELFLTAVKLTHDDTGARYLHLAREDTNNLFSVQFRTTPMDSTGVPHILEHTVLCGSQKYPCRDPFFKMLNRSLSTFMNAFTASDYTLYPFSTQNPKDFQNLLSVYLDATFFPCLRELDFWQEGWRLEHENPSDPQTPLVFKGVVFNEMKGAFTDNERIFSQHLQNRLLPDHTYSVVSGGDPLCIPELTWEQLKQFHATHYHPSNARFFTYGNFPLEQHLKQIHEEALSKFQKIEPSTVVPAQTPWDKPREFQITCGPDSFATDPSKQTTVSVSFLLPDITDTFEAFTLSLLSSLLTSGPNSPFYKALIESGLGTDFSPDVGYNGYTREAYFSVGLQGIVEKDIETVRSLIDRTIDEVVEKGFEDDRIEALLHKIEIQMKHQSTSFGLMLTSYIASCWNHDGDPVELLKLGNQLAKFRQCLQENPKFLQEKVKQYFKNNQHKLTLSMRPDDKYHEKQAQVEATKLKQKVEALSPGDRQQIYEKGLELRSQQSKPQDASCLPALKVSDIEPTIPVTELDVVLTAGDIPVQYCAQPTNGMVYFRAFSSLNTLPEELRPYVPLFCSVLTKLGCGLLDYREQAQQIELKTGGMSASPHVLPDDSHMDTYEQGVLFSSLCLDRNLPDMMQLWSEIFNNPCFEEEEHFKVLVKMTAQELANGIPDSGHLYASIRAGRTLTPAGDLQETFSGMDQVRLMKRIAEMTDIKPILRKLPRIKKHLLNGDNMRCSVNATPQQMPQTEKAVEDFLRSIGRSKKERRPVRPHTVEKPVPSSSGGDAHVPHGSQVIRKLVMEPTFKPWQMKTHFLMPFPVNYVGECIRTVPYTDPDHASLKILARLMTAKFLHTEIREKGGAYGGGAKLSHNGIFTLYSYRDPNTIETLQSFGKAVDWAKSGKFTQQDIDEAKLSVFSTVDAPVAPSDKGMDHFLYGLSDEMKQAHREQLFAVSHDKLLAVSDRYLGTGKSTHGLAILGPENPKIAKDPSWIIR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6xosA01
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	6xosA02
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	6xosA03
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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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.70 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	130572

fit	/app/data/saxs_computation/xo/6xos/6xos.fit
pddf	/app/data/pr_computation/xo/6xos/6xos.pr.out
profile	/app/data/saxs_computation/xo/6xos/6xos.dat

CryoEM structure of human presequence protease in partial open state 1

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D