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8kb4

Cryo-EM structure of human TMEM87A A308M

Method: ELECTRON MICROSCOPY Dmax: 100.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transmembrane protein 87A,EGFP

Human adenovirus C serotype 2

UniProt A0A6M5E0N3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2–239 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

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 8KB4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7U8G Cryo-EM structure of the core human NADPH oxidase NOX2 Deposited 2022-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–239（239 aa） Fragment：N-terminal 2x streptag followed by EGFP and TEV + thrombin cleavage sites.
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；0.03% DDM, 150 mM NaCl, 20 mM Tris
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8HTT Cryo-EM structure of human TMEM87A, gluconate-bound Deposited 2022-12-21 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–239（238 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
8U1U Structure of a class A GPCR/agonist complex Deposited 2023-09-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–239（239 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
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 A0A6M5E0N3_ADE02
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 577–814； UniProt 2–239

Transmembrane protein 87A,EGFP

Human adenovirus C serotype 2

UniProt Q8NBN3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–555 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

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 8KB4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8CTJ Cryo-EM structure of TMEM87A Deposited 2022-05-15 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–555（555 aa）
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
8HSI Cryo-EM structure of human TMEM87A, PE-bound Deposited 2022-12-19 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions 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 mutation/modification Different oligomeric state Different ligand/ion 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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 8kb4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8kb4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8kb4
Deposition date deposition_date2023-08-03
Structure title titleCryo-EM structure of human TMEM87A A308M
Keywords keywordsnon-selective cation channel, ion channel, membrane protein, Golgi-localized protein; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.90 Å
Radius of gyration Rg (electron density) rg_electron28.42 Å
Forward intensity I(0) i031605900.00
Molecular weight molecular_weight47716.0 kDa
Excluded volume excluded_volume61602 ų
Envelope volume envelope_volume80811 ų
Hydration-shell volume shell_volume25914 ų
Envelope diameter envelope_diameter105.8 Å
Shell Rg shell_rg33.08 Å
Envelope Rg envelope_rg28.29 Å
Shape Rg shape_rg28.39 Å
Total Rg total_rg29.11 Å
Total atoms total_atoms3410
Residues n_residues402
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax100.8 Å
Rg (real space) rg_real29.16 Å
Rg uncertainty (real space) rg_real_error0.87 Å
I(0) (real space) i0_real3.1610e+07
I(0) uncertainty (real space) i0_real_error5.3340e+05
Rg (reciprocal space) rg_reciprocal29.05 Å
I(0) (reciprocal space) i0_reciprocal31600000.0000
Solution quality estimate total_estimate0.8116
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.5 Å
Skewness Skewness skewness0.573
Kurtosis Kurtosis kurtosis-0.316
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4965000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.649; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.627; Smooth: 0.972
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)