SAXSdb — 8k1d

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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 301–827 Chain B； UniProt 301–827	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.53 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 8K1D	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
8K13 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 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 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
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 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 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 1–484； UniProt 301–827 Author chain B； PDBConstruct 1–484； UniProt 301–827

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	8k1d
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	29.43 Å
Radius of gyration Rg (electron density) rg_electron	28.88 Å
Forward intensity I(0) i0	62749900.00
Molecular weight molecular_weight	69299.0 kDa
Excluded volume excluded_volume	89862 Å³
Envelope volume envelope_volume	122150 Å³
Hydration-shell volume shell_volume	35377 Å³
Envelope diameter envelope_diameter	93.5 Å
Shell Rg shell_rg	35.93 Å
Envelope Rg envelope_rg	28.69 Å
Shape Rg shape_rg	28.84 Å
Total Rg total_rg	29.91 Å
Total atoms total_atoms	4902
Residues n_residues	610
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	91.3 Å
Rg (real space) rg_real	29.35 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	6.2750e+07
I(0) uncertainty (real space) i0_real_error	9.4820e+05
Rg (reciprocal space) rg_reciprocal	29.38 Å
I(0) (reciprocal space) i0_reciprocal	62750000.0000
Solution quality estimate total_estimate	0.9118
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.190
Kurtosis Kurtosis kurtosis	-0.552
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8422000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.966; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.954

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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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	3.53 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	81463

Description description	SID1 transmembrane family member 1
Molecular weight formula_weight	58291.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4902

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/k1/8k1d/8k1d.fit
pddf	/app/data/pr_computation/k1/8k1d/8k1d.pr.out
profile	/app/data/saxs_computation/k1/8k1d/8k1d.dat