SAXSdb — 8kcx

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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 8 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–827 Chain C； UniProt 1–827	Not recorded	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.96 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 8KCX	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 experimental conditions 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–827（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 mutation/modification 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 1–827（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 experimental conditions 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 experimental conditions 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 experimental conditions 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 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
8V38 Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) Deposited 2023-11-27	Different oligomeric state Different ligand/ion Different experimental conditions 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 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	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 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	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 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	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–827； UniProt 1–827 Author chain C； PDBConstruct 1–827； UniProt 1–827

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	8kcx
Deposition date deposition_date	2023-08-08
Structure title title	Cryo-EM structure of human SIDT1
Keywords keywords	Membrane protein; MEMBRANE 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	36.53 Å
Radius of gyration Rg (electron density) rg_electron	36.31 Å
Forward intensity I(0) i0	235071000.00
Molecular weight molecular_weight	134430.0 kDa
Excluded volume excluded_volume	172350 Å³
Envelope volume envelope_volume	233830 Å³
Hydration-shell volume shell_volume	53033 Å³
Envelope diameter envelope_diameter	125.3 Å
Shell Rg shell_rg	42.89 Å
Envelope Rg envelope_rg	36.50 Å
Shape Rg shape_rg	36.29 Å
Total Rg total_rg	36.88 Å
Total atoms total_atoms	9486
Residues n_residues	1142
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	122.0 Å
Rg (real space) rg_real	36.58 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	2.3510e+08
I(0) uncertainty (real space) i0_real_error	3.5350e+06
Rg (reciprocal space) rg_reciprocal	36.55 Å
I(0) (reciprocal space) i0_reciprocal	235100000.0000
Solution quality estimate total_estimate	0.6817
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	39.7 Å
Skewness Skewness skewness	0.401
Kurtosis Kurtosis kurtosis	-0.329
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	55620000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.855; Stabil: 1.000; Sysdev: 0.159; Positv: 1.000; Valcen: 0.974; Smooth: 0.843

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	SID1 transmembrane family member 1
Molecular weight formula_weight	96877.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	9486

MRGCLRLALLCALPWLLLAASPGHPAKSPRQPPAPRRDPFDAARGADFDHVYSGVVNLSTENIYSFNYTSQPDQVTAVRVYVNSSSENLNYPVLVVVRQQKEVLSWQVPLLFQGLYQRSYNYQEVSRTLCPSEATNETGPLQQLIFVDVASMAPLGAQYKLLVTKLKHFQLRTNVAFHFTASPSQPQYFLYKFPKDVDSVIIKVVSEMAYPCSVVSVQNIMCPVYDLDHNVEFNGVYQSMTKKAAITLQKKDFPGEQFFVVFVIKPEDYACGGSFFIQEKENQTWNLQRKKNLEVTIVPSIKESVYVKSSLFSVFIFLSFYLGCLLVGFVHYLRFQRKSIDGSFGSNDGSGNMVASHPIAASTPEGSNYGTIDESSSSPGRQMSSSDGGPPGQSDTDSSVEESDFDTMPDIESDKNIIRTKMFLYLSDLSRKDRRIVSKKYKIYFWNIITIAVFYALPVIQLVITYQTVVNVTGNQDICYYNFLCAHPLGVLSAFNNILSNLGHVLLGFLFLLIVLRRDILHRRALEAKDIFAVEYGIPKHFGLFYAMGIALMMEGVLSACYHVCPNYSNFQFDTSFMYMIAGLCMLKLYQTRHPDINASAYSAYASFAVVIMVTVLGVVFGKNDVWFWVIFSAIHVLASLALSTQIYYMGRFKIDLGIFRRAAMVFYTDCIQQCSRPLYMDRMVLLVVGNLVNWSFALFGLIYRPRDFASYMLGIFICNLLLYLAFYIIMKLRSSEKVLPVPLFCIVATAVMWAAALYFFFQNLSSWEGTPAESREKNRECILLDFFDDHDIWHFLSATALFFSFLVLLTLDDDLDVVRRDQIPVFENLYFQGDYKDDDDKHHHHHHHH

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	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 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 4 Entity 4 non-polymer

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

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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	2.96 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	62617

fit	/app/data/saxs_computation/kc/8kcx/8kcx.fit
pddf	/app/data/pr_computation/kc/8kcx/8kcx.pr.out
profile	/app/data/saxs_computation/kc/8kcx/8kcx.dat

Cryo-EM structure of human SIDT1

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