8woq

Cryo-EM structure of human SIDT1 protein with C1 symmetry at neutral pH

Method: ELECTRON MICROSCOPY D_max: 128.8 Å Quality: GOOD

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

SID1 transmembrane family member 1

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	Other combination Homooligomer Protein × 2 其他Polymer 4 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–832 Chain B； UniProt 1–832	Not recorded	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 2 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CLR CHOLESTEROL × 15 OLA OLEIC ACID × 2 SPL OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.85 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 8WOQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8J6M SIDT1 protein Deposited 2023-04-26	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–827（808 aa） Chain B 20–827（808 aa）	Not recorded	CLR CHOLESTEROL × 8 ZN ZINC ION × 2 NA SODIUM ION × 1 OLA OLEIC ACID × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.77 Å
8JUL Cryo-EM structure of SIDT1 in complex with phosphatidic acid Deposited 2023-06-26	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–827（827 aa） Chain B 1–827（827 aa）	Not recorded	ZN ZINC ION × 2 PX2 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.92 Å
8JUN Cryo-EM structure of SIDT1 E555Q mutant Deposited 2023-06-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–827（827 aa） Chain B 1–827（827 aa）	Mutation：E555Q Mutation：E555Q	ZN ZINC ION × 2 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.38 Å
8K13 SID1 transmembrane family member 1 Deposited 2023-07-10	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 21–827（807 aa） Chain B 21–827（807 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
8K1B SID1 transmembrane family member 1 Deposited 2023-07-10	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 47–300（254 aa） Chain B 47–300（254 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å
8K1D SID1 transmembrane family member 1 Deposited 2023-07-10	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 301–827（527 aa） Chain B 301–827（527 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.53 Å
8KCW Cryo-EM structure of human SIDT1 bound to cholesterol Deposited 2023-08-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–827（827 aa） Chain C 1–827（827 aa）	Not recorded	ZN ZINC ION × 2 CLR CHOLESTEROL × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.77 Å
8KCX Cryo-EM structure of human SIDT1 Deposited 2023-08-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–827（827 aa） Chain C 1–827（827 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
8V38 Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) Deposited 2023-11-27	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–827（827 aa） Chain B 1–827（827 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8WOR Cryo-EM structure of human SIDT1 protein with C2 symmetry at neutral pH Deposited 2023-10-07	Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–832（832 aa） Chain B 1–832（832 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CLR CHOLESTEROL × 15 OLA OLEIC ACID × 2 SPL OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.66 Å
8WOS Cryo-EM structure of human SIDT1 protein with C1 symmetry at low pH Deposited 2023-10-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–832（832 aa） Chain B 1–832（832 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CLR CHOLESTEROL × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 5.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
8WOT Cryo-EM structure of human SIDT1 protein with C2 symmetry at low pH Deposited 2023-10-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–832（832 aa） Chain B 1–832（832 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CLR CHOLESTEROL × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 5.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
9M8U Cryo-EM structure of human SIDT1 Deposited 2025-03-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–832（832 aa） Chain B 1–832（832 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.79 Å

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SIDT1_HUMAN
Isoform	Q9NXL6-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–832； UniProt 1–832 Author chain B； PDBConstruct 1–832； UniProt 1–832

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8woq
Deposition date deposition_date	2023-10-07
Structure title title	Cryo-EM structure of human SIDT1 protein with C1 symmetry at neutral pH
Keywords keywords	Ceramidase, putative RNA and cholesterol transport protein, 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	38.42 Å
Radius of gyration Rg (electron density) rg_electron	37.62 Å
Forward intensity I(0) i0	292413000.00
Molecular weight molecular_weight	158470.0 kDa
Excluded volume excluded_volume	206290 Å³
Envelope volume envelope_volume	271720 Å³
Hydration-shell volume shell_volume	59239 Å³
Envelope diameter envelope_diameter	128.4 Å
Shell Rg shell_rg	44.22 Å
Envelope Rg envelope_rg	37.78 Å
Shape Rg shape_rg	37.60 Å
Total Rg total_rg	38.16 Å
Total atoms total_atoms	11196
Residues n_residues	1294
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	128.8 Å
Rg (real space) rg_real	38.50 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	2.9240e+08
I(0) uncertainty (real space) i0_real_error	4.9670e+06
Rg (reciprocal space) rg_reciprocal	38.46 Å
I(0) (reciprocal space) i0_reciprocal	292400000.0000
Solution quality estimate total_estimate	0.8746
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	40.8 Å
Skewness Skewness skewness	0.410
Kurtosis Kurtosis kurtosis	-0.353
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	65520000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.853

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	SID1 transmembrane family member 1
Molecular weight formula_weight	99695.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11218

MRGCLRLALLCALPWLLLAASPGHPAKSPRQPPAPRRDPFDAARGADFDHVYSGVVNLSTENIYSFNYTSQPDQVTAVRVYVNSSSENLNYPVLVVVRQQKEVLSWQVPLLFQGLYQRSYNYQEVSRTLCPSEATNETGPLQQLIFVDVASMAPLGAQYKLLVTKLKHFQLRTNVAFHFTASPSQPQYFLYKFPKDVDSVIIKVVSEMAYPCSVVSVQNIMCPVYDLDHNVEFNGVYQSMTKKAAITLQKKDFPGEQFFVVFVIKPEDYACGGSFFIQEKENQTWNLQRKKNLEVTIVPSIKESVYVKSSLFSVFIFLSFYLGCLLVGFVHYLRFQRKSIDGSFGSNDGSGNMVASHPIAASTPEGSNYGTIDESSSSPGRQMSSSDGGPPGQSDTDSSVEESDFDTMPDIESDKNIIRTKMFLYLSDLSRKDRRIVSKKYKIYFWNIITIAVFYALPVIQLVITYQTVVNVTGNQDICYYNFLCAHPLGVLSAFNNILSNLGHVLLGFLFLLIVLRRDILHRRALEAKDIFAVEYGIPKHFGLFYAMGIALMMEGVLSACYHVCPNYSNFQFDTSFMYMIAGLCMLKLYQTRHPDINASAYSAYASFAVVIMVTVLGVVFGKNDVWFWVIFSAIHVLASLALSTQIYYMGRFKIDVSDTDLGIFRRAAMVFYTDCIQQCSRPLYMDRMVLLVVGNLVNWSFALFGLIYRPRDFASYMLGIFICNLLLYLAFYIIMKLRSSEKVLPVPLFCIVATAVMWAAALYFFFQNLSSWEGTPAESREKNRECILLDFFDDHDIWHFLSATALFFSFLVLLTLDDDLDVVRRDQIPVFSRENLYFQGSGWSHPQFEKGGGSGGGSGGSAWSHPQFEKGSDYKDDDDK

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	Homo sapiens

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	CHOLESTEROL
Molecular weight formula_weight	386.7 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 7 Entity 7 non-polymer

Description description	OLEIC ACID
Molecular weight formula_weight	282.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE
Molecular weight formula_weight	425.7 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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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	2.85 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	503286

fit	/app/data/saxs_computation/wo/8woq/8woq.fit
pddf	/app/data/pr_computation/wo/8woq/8woq.pr.out
profile	/app/data/saxs_computation/wo/8woq/8woq.dat