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9grz

Cryo-EM structure of human SLC35B1 with AMP-PNP

Method: ELECTRON MICROSCOPY Dmax: 67.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Solute carrier family 35 member B1

Homo sapiens

UniProt P78383

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 B； UniProt 1–322 Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.40 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 9GRZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9GS5 Cryo-EM structure of human SLC35B1-E33A variant with ADP in outward facing conformation Deposited 2024-09-13 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–322（322 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9GS7 Cryo-EM structure of human SLC35B1-E33A variant with AMP-PNP Deposited 2024-09-13 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–322（322 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
9GSL Cryo-EM structure of human SLC35B1 in inward facing conformation Deposited 2024-09-16 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–322（322 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
9I20 Cryo-EM structure of human SLC35B1 with ADP Deposited 2025-01-17 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–322（322 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 1 PEV (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name S35B1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 1–322； UniProt 1–322

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 9grz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9grz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9grz
Deposition date deposition_date2024-09-13
Structure title titleCryo-EM structure of human SLC35B1 with AMP-PNP
Keywords keywordsATP:ADP exchanger, AXER, AMP-PNP, membrane protein, TRANSPORT PROTEIN; TRANSPORT 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_guinier20.45 Å
Radius of gyration Rg (electron density) rg_electron19.94 Å
Forward intensity I(0) i016246000.00
Molecular weight molecular_weight33449.0 kDa
Excluded volume excluded_volume43320 ų
Envelope volume envelope_volume53562 ų
Hydration-shell volume shell_volume22185 ų
Envelope diameter envelope_diameter67.5 Å
Shell Rg shell_rg26.80 Å
Envelope Rg envelope_rg20.29 Å
Shape Rg shape_rg19.97 Å
Total Rg total_rg20.95 Å
Total atoms total_atoms4794
Residues n_residues295
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 dmax67.7 Å
Rg (real space) rg_real20.36 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real1.6250e+07
I(0) uncertainty (real space) i0_real_error2.1730e+05
Rg (reciprocal space) rg_reciprocal20.38 Å
I(0) (reciprocal space) i0_reciprocal16250000.0000
Solution quality estimate total_estimate0.6484
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.2 Å
Skewness Skewness skewness0.235
Kurtosis Kurtosis kurtosis-0.345
Angular range angular_range— – 0.3900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2847000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 0.319; Positv: 1.000; Valcen: 0.999; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)