SAXSdb — 1y4e

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

Sodium/hydrogen exchanger 1

Homo sapiens

UniProt P19634

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 155–180	Fragment：Transmembrane segment IV Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	SOLUTION NMR NMR measurement conditions：303 K；Pressure ambient NMR sample composition：2 mM TM IV, unlabelled; 1 mM DSS, CDCl3:CD3OH:H2O (4:4:1 v:v:v) \| CDCl3:CD3OH:H2O (4:4:1 v:v:v) NMR sample composition：2 mM TM IV, U-15N; 1 mM DSS, CDCl3:CD3OH:H2O (4:4:1 v:v:v) \| CDCl3:CD3OH:H2O (4:4:1 v:v:v)	Resolution not provided

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 1Y4E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
23XK Cryo-EM structure of human sodium/proton antiporter NHE1 in complex with Cariporide in an outward-open conformation Deposited 2026-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–815（815 aa） Chain B 1–815（815 aa）	Not recorded	HG0 N-[bis(azanyl)methylidene]-3-methylsulfonyl-4-propan-2-yl-benzamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
23XM Cryo-EM structure of human sodium/proton antiporter NHE1 in complex with Eniporide in an outward-open conformation Deposited 2026-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–815（815 aa） Chain B 1–815（815 aa）	Not recorded	A1E6D Eniporide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
23XO Cryo-EM structure of human sodium/proton antiporter NHE1 in complex with Rimeporide in an outward-open conformation Deposited 2026-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–815（815 aa） Chain B 1–815（815 aa）	Not recorded	A1E6E ~{N}-carbamimidoyl-2-methyl-4,5-bis(methylsulfonyl)benzamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
2BEC Crystal structure of CHP2 in complex with its binding region in NHE1 and insights into the mechanism of pH regulation Deposited 2005-10-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 503–545（43 aa） Fragment：residues 503-545	Not recorded	YT3 YTTRIUM (III) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% PEG 3350, 0.2M ammonium acetate, 0.1M Bis-Tris, 0.01M yttrium chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.287
2E30 Solution structure of the cytoplasmic region of Na+/H+ exchanger 1 complexed with essential cofactor calcineurin B homologous protein 1 Deposited 2006-11-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 503–545（43 aa） Fragment：NHE1 fragment (503-545)	Not recorded	CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 6.9；310 K；Ionic strength (raw mmCIF value) 30mM；Pressure ambient NMR sample composition 0.9mM CHP1/NHE1 U-15N, U-13C, 50mM Tris buffer, 99% D2O \| 99% D2O NMR sample composition 0.5mM CHP1/NHE1 60%2H, U-15N, U-13C, 50mM Tris buffer, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 0.9mM CHP1/NHE1 U-15N, 50mM Tris buffer, 95% H2Om, 5% D2O \| 95% H2O/5% D2O NMR sample composition 0.9mM CHP1/NHE1 U-15N, U-13C, 50mM Tris buffer, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5mM CHP1/NHE1 U-15N, 15%-13C, 50mM Tris buffer, 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
2HTG Structural and functional characterization of TM VII of the NHE1 isoform of the Na+/H+ exchanger Deposited 2006-07-25	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 250–274（25 aa） Fragment：Transmembrane segment VII	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.8；303 K；Ionic strength (raw mmCIF value) ~ 75 mM Na+/DPC-；Pressure ambient NMR sample composition ~ 1 mM peptide synthetic source 1 (unlabeled), 90% H2O/10% D2O, ~ 75 mM dodecylphosphocholine, 1.0 mM DSS \| 90% H2O/10% D2O NMR sample composition ~ 1 mM peptide synthetic source 2 (6 specific 15N labels), 90% H2O/10% D2O, ~ 75 mM dodecylphosphocholine, 1.0 mM DSS \| 90% H2O/10% D2O	Resolution not provided
2KBV Structural and functional analysis of TM XI of the NHE1 isoform of thE NA+/H+ exchanger Deposited 2008-12-09	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 447–472（26 aa） Fragment：NHE1 transmembrane segment XI	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；303 K；Pressure ambient NMR sample composition 150 mM DPC-1, 0.25 mM DSS-2, 2 mM TMXI-3, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2L0E Structural and functional analysis of tm vi of the nhe1 isoform of the na+/h+ exchanger Deposited 2010-07-01	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 226–250（25 aa） Fragment：transmembrane segment VI of NHE1, UNP residues 226-250	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；303 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 2 mM TM VI-1, 0.25 mM DSS-2, 150 mM [U-2H] DPC-3, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2MDF NMR structure of a two-transmembrane segment TM VI-VII of NHE1 Deposited 2013-09-10	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 226–274（49 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；303 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1-2 mM [U-15N] entity, 5 % [U-2H] D2O, 0.25 mM [1,1,2,2,3,3-2H6] DSS, 95 % H2O, 75-150 mM [U-2H] dodecylphosphocholine, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1-2 mM [U-15N] entity, 100 % [U-2H] D2O, 0.25 mM [1,1,2,2,3,3-2H6] DSS, 75-150 mM [U-2H] dodecylphosphocholine, 100% D2O \| 100% D2O	Resolution not provided
2YGG Complex of CaMBR and CaM Deposited 2011-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 622–689（68 aa） Fragment：CAM BINDING REGION, RESIDUES 622-689	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 3 CA CALCIUM ION × 4 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.23 Å R-free 0.232
6NUC Structure of Calcineurin in complex with NHE1 peptide Deposited 2019-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 679–723（45 aa）	Not recorded	FE FE (III) ION × 1 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 NA SODIUM ION × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；298 K；40% (v/v) PEG 600, 100 mM CHES/ Sodium hydroxide pH 9.5, 0.2 M MgCl2	Resolution 1.90 Å R-free 0.194
6NUF Structure of Calcineurin in complex with NHE1 peptide Deposited 2019-01-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 679–723（45 aa）	Mutation：R698A, R700A	FE FE (III) ION × 1 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 PGE TRIETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1 NA SODIUM ION × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；40% (v/v) PEG 600, 100 mM CHES/ Sodium hydroxide pH 9.5, 0.2 M MgCl2	Resolution 1.90 Å R-free 0.209
6NUU Structure of Calcineurin mutant in complex with NHE1 peptide Deposited 2019-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 679–723（45 aa）	Not recorded	FE FE (III) ION × 1 ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；298 K；40% (v/v) PEG 600, 100 mM CHES/ Sodium hydroxide pH 9.5, 0.2 M MgCl2	Resolution 2.30 Å R-free 0.243
6ZBI Ternary complex of Calmodulin bound to 2 molecules of NHE1 Deposited 2020-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 622–657（36 aa） Chain C 622–657（36 aa）	Not recorded	CA CALCIUM ION × 4	SOLUTION NMR NMR measurement conditions pH 7.5；310 K；Ionic strength (raw mmCIF value) 120；Pressure 1 NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] Calmodulin, 1.15 mM Sodium/Hydrogen exchanger 1 (NHE1, SLC9A1), 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1 mM [U-99% 13C; U-99% 15N] Sodium/Hydrogen exchanger 1 (NHE1, SLC9A1), 0.5 mM Calmodulin, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7DSV Structure of a human NHE1-CHP1 complex under pH 6.5 Deposited 2021-01-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 87–558（472 aa） Chain B 87–558（472 aa）	Not recorded	LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 16	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7DSW Structure of a human NHE1-CHP1 complex under pH 7.5 Deposited 2021-01-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 87–506（420 aa） Chain B 87–506（420 aa）	Not recorded	LBN 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7DSX Structure of a human NHE1-CHP1 complex under pH 7.5, bound by cariporide Deposited 2021-01-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 85–593（509 aa） Chain B 85–593（509 aa）	Not recorded	PGT (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE × 6 HG0 N-[bis(azanyl)methylidene]-3-methylsulfonyl-4-propan-2-yl-benzamide × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9NXE Crystal Structure of Calcineurin Clinical Variant E282K Deposited 2025-03-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 679–723（45 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1 FE FE (III) ION × 1 ZN ZINC ION × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；290 K；0.1 M CAPS pH 9, 0.2 M MgCl2 and 24% PEG 600	Resolution 2.09 Å R-free 0.243

18 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SL9A1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–26； UniProt 155–180

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	1y4e
Deposition date deposition_date	2004-11-30
Structure title title	NMR structure of transmembrane segment IV of the NHE1 isoform of the Na+/H+ exchanger
Keywords keywords	NHE1 isoform, transmembrane, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	10.66 Å
Radius of gyration Rg (electron density) rg_electron	11.35 Å
Forward intensity I(0) i0	780049000.00
Molecular weight molecular_weight	313880.0 kDa
Excluded volume excluded_volume	421660 Å³
Envelope volume envelope_volume	28123 Å³
Hydration-shell volume shell_volume	15163 Å³
Envelope diameter envelope_diameter	50.0 Å
Shell Rg shell_rg	21.56 Å
Envelope Rg envelope_rg	15.65 Å
Shape Rg shape_rg	11.37 Å
Total Rg total_rg	11.50 Å
Total atoms total_atoms	45800
Residues n_residues	2600
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	41.7 Å
Rg (real space) rg_real	10.72 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	7.8000e+08
I(0) uncertainty (real space) i0_real_error	9.1820e+06
Rg (reciprocal space) rg_reciprocal	10.71 Å
I(0) (reciprocal space) i0_reciprocal	780000000.0000
Solution quality estimate total_estimate	0.7952
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	13.2 Å
Skewness Skewness skewness	0.246
Kurtosis Kurtosis kurtosis	-0.578
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7402.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.652; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.405; Smooth: 0.973

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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 (2)

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Description description	Sodium/hydrogen exchanger 1
Molecular weight formula_weight	3139.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	45800

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	Escherichia coli

fit	/app/data/saxs_computation/y4/1y4e/1y4e.fit
pddf	/app/data/pr_computation/y4/1y4e/1y4e.pr.out
profile	/app/data/saxs_computation/y4/1y4e/1y4e.dat

NMR structure of transmembrane segment IV of the NHE1 isoform of the Na+/H+ exchanger

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

Sodium/hydrogen exchanger 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)