SAXSdb — 8k13

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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	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 21–827 Chain B； UniProt 21–827	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

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 8K13	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 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 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
8K1B SID1 transmembrane family member 1 Deposited 2023-07-10	Different construct 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 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
8WOQ Cryo-EM structure of human SIDT1 protein with C1 symmetry at neutral pH Deposited 2023-10-07	Different construct Different oligomeric state Different ligand/ion 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 2.85 Å
8WOR Cryo-EM structure of human SIDT1 protein with C2 symmetry at neutral pH Deposited 2023-10-07	Different construct Different oligomeric state Different ligand/ion 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 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 1–832（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 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 1–832（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 construct 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	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–781； UniProt 21–827 Author chain B； PDBConstruct 18–781； UniProt 21–827

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	8k13
Deposition date deposition_date	2023-07-10
Structure title title	SID1 transmembrane family member 1
Keywords keywords	VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	35.33 Å
Radius of gyration Rg (electron density) rg_electron	35.26 Å
Forward intensity I(0) i0	216665000.00
Molecular weight molecular_weight	128440.0 kDa
Excluded volume excluded_volume	164660 Å³
Envelope volume envelope_volume	221670 Å³
Hydration-shell volume shell_volume	51661 Å³
Envelope diameter envelope_diameter	117.1 Å
Shell Rg shell_rg	42.11 Å
Envelope Rg envelope_rg	35.32 Å
Shape Rg shape_rg	35.22 Å
Total Rg total_rg	35.95 Å
Total atoms total_atoms	9078
Residues n_residues	1118
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	117.3 Å
Rg (real space) rg_real	35.31 Å
Rg uncertainty (real space) rg_real_error	0.95 Å
I(0) (real space) i0_real	2.1670e+08
I(0) uncertainty (real space) i0_real_error	3.7390e+06
Rg (reciprocal space) rg_reciprocal	35.33 Å
I(0) (reciprocal space) i0_reciprocal	216700000.0000
Solution quality estimate total_estimate	0.8858
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.7 Å
Skewness Skewness skewness	0.341
Kurtosis Kurtosis kurtosis	-0.358
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	41070000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.915

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	SID1 transmembrane family member 1
Molecular weight formula_weight	91771.9 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	9078

MKANLLVLLCALAAADASPGHPAKSPRQPPAPRRDPFDAARGADFDHVYSGVVNLSTENIYSFNYTSQPDQVTAVRVYVNSSSENLNYPVLVVVRQQKEVLSWQVPLLFQGLYQRSYNYQEVSRTLCPSEATNETGPLQQLIFVDVASMAPLGAQYKLLVTKLKHFQLRTNVAFHFTASPSQPQYFLYKFPKDVDSVIIKVVSEMAYPCSVVSVQNIMCPVYDLDHNVEFNGVYQSMTKKAAITLQKKDFPGEQFFVVFVIKPEDYACGGSFFIQEKENQTWNLQRKKNLEVTIVPSIKESVYVKSSLFSVFIFLSFYLGCLLVGFVHYLRFQRKSIDGSFGSNDGSGNMVASHPIAASTPEPDIESDKNIIRTKMFLYLSDLSRKDRRIVSKKYKIYFWNIITIAVFYALPVIQLVITYQTVVNVTGNQDICYYNFLCAHPLGVLSAFNNILSNLGHVLLGFLFLLIVLRRDILHRRALEAKDIFAVEYGIPKHFGLFYAMGIALMMEGVLSACYHVCPNYSNFQFDTSFMYMIAGLCMLKLYQTRHPDINASAYSAYASFAVVIMVTVLGVVFGKNDVWFWVIFSAIHVLASLALSTQIYYMGRFKIDLGIFRRAAMVFYTDCIQQCSRPLYMDRMVLLVVGNLVNWSFALFGLIYRPRDFASYMLGIFICNLLLYLAFYIIMKLRSSEKVLPVPLFCIVATAVMWAAALYFFFQNLSSWEGTPAESREKNRECILLDFFDDHDIWHFLSATALFFSFLVLLTLDDDLDVVRRDQIPVFDYKDHDGDYKDHDIDYKDDDDK

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	Spodoptera frugiperda

Entity 2 Entity 2 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	6

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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	3.33 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	149089

fit	/app/data/saxs_computation/k1/8k13/8k13.fit
pddf	/app/data/pr_computation/k1/8k13/8k13.pr.out
profile	/app/data/saxs_computation/k1/8k13/8k13.dat

SID1 transmembrane family member 1

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

SID1 transmembrane family member 1

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)