SAXSdb — 8ctj

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

Transmembrane protein 87A

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 1–555	Not recorded	PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.74 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 8CTJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8HSI Cryo-EM structure of human TMEM87A, PE-bound Deposited 2022-12-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–555（555 aa）	Not recorded	L9Q (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 1 CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 9；50mM Tris pH 9.0, 250mM NaCl, 0.01% (w/v) LMNG, 0.002% (w/v) CHS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8HTT Cryo-EM structure of human TMEM87A, gluconate-bound Deposited 2022-12-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–555（555 aa）	Not recorded	GCO D-gluconic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 9；50mM HEPES pH 7.5, 250mM NaCl, 0.01% (w/v) LMNG, 0.002% (w/v) CHS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8KB4 Cryo-EM structure of human TMEM87A A308M Deposited 2023-08-03	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–555（555 aa）	Mutation：A308M	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 65I (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 9；50mM HEPES pH 7.5, 250mM NaCl, 0.01% (w/v) LMNG, 0.002% (w/v) CHS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TM87A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–555； UniProt 1–555

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	8ctj
Deposition date deposition_date	2022-05-15
Structure title title	Cryo-EM structure of TMEM87A
Keywords keywords	GOLD domain, transport, 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	28.16 Å
Radius of gyration Rg (electron density) rg_electron	27.72 Å
Forward intensity I(0) i0	30544300.00
Molecular weight molecular_weight	46878.0 kDa
Excluded volume excluded_volume	60551 Å³
Envelope volume envelope_volume	78382 Å³
Hydration-shell volume shell_volume	25657 Å³
Envelope diameter envelope_diameter	100.2 Å
Shell Rg shell_rg	32.58 Å
Envelope Rg envelope_rg	27.78 Å
Shape Rg shape_rg	27.70 Å
Total Rg total_rg	28.40 Å
Total atoms total_atoms	3312
Residues n_residues	401
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	96.5 Å
Rg (real space) rg_real	28.51 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	3.0540e+07
I(0) uncertainty (real space) i0_real_error	5.1490e+05
Rg (reciprocal space) rg_reciprocal	28.40 Å
I(0) (reciprocal space) i0_reciprocal	30540000.0000
Solution quality estimate total_estimate	0.8263
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.587
Kurtosis Kurtosis kurtosis	-0.266
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5365000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.699; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.744; Smooth: 0.898

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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	Transmembrane protein 87A
Molecular weight formula_weight	64512.9 kDa
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	3312

MAAAAWLQVLPVILLLLGAHPSPLSFFSAGPATVAAADRSKWHIPIPSGKNYFSFGKILFRNTTIFLKFDGEPCDLSLNITWYLKSADCYNEIYNFKAEEVELYLEKLKEKRGLSGKYQTSSKLFQNCSELFKTQTFSGDFMHRLPLLGEKQEAKENGTNLTFIGDKTAMHEPLQTWQDAPYIFIVHIGISSSKESSKENSLSNLFTMTVEVKGPYEYLTLEDYPLMIFFMVMCIVYVLFGVLWLAWSACYWRDLLRIQFWIGAVIFLGMLEKAVFYAEFQNIRYKGESVQGALILAELLSAVKRSLARTLVIIVSLGYGIVKPRLGVTLHKVVVAGALYLLFSGMEGVLRVTGAQTDLASLAFIPLAFLDTALCWWIFISLTQTMKLLKLRRNIVKLSLYRHFTNTLILAVAASIVFIIWTTMKFRIVTCQSDWRELWVDDAIWRLLFSMILFVIMVLWRPSANNQRFAFSPLSEEEEEDEQKEPMLKESFEGMKMRSTKQEPNGNSKVNKAQEDDLKWVEENVPSSVTDVALPALLDSDEERMITHFERSKMESNSLEVLFQ

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	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Molecular weight formula_weight	744.0 kDa
Source method src_method	syn
Copy count entity_count	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	triclinic

Resolution resolution	4.74 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	138217

fit	/app/data/saxs_computation/ct/8ctj/8ctj.fit
pddf	/app/data/pr_computation/ct/8ctj/8ctj.pr.out
profile	/app/data/saxs_computation/ct/8ctj/8ctj.dat

Cryo-EM structure of TMEM87A

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

Transmembrane protein 87A

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)