SAXSdb — 2k60

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

PROTEIN (Stromal interaction molecule 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	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 58–201	Fragment：UNP residues 58-201	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions：pH 8；293 K；Ionic strength (raw mmCIF value) 105；Pressure 1 NMR measurement conditions：293 K；Ionic strength (raw mmCIF value) 105；Pressure 1 NMR sample composition：0.5-1.0 mM [U-100% 13C; U-100% 15N] stromal interaction molecule 1, 20 mM TRIS, 100 mM sodium chloride, 5 mM CALCIUM ION, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：0.5-1.0 mM [U-100% 13C; U-100% 15N] stromal interaction molecule 1, 20 mM [U-99% 2H] TRIS, 100 mM sodium chloride, 5 mM CALCIUM ION, 100% D2O \| 100% D2O	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 2K60	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MAJ Solution Structure of the STIM1 CC1-CC2 homodimer. Deposited 2013-07-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 312–387（76 aa） Fragment：UNP residues 312-387 Chain C 312–387（76 aa） Fragment：UNP residues 312-387	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；308 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition 0.5 mM [U-99% 15N] protein, 20 mM bis-TRIS, 0.175 v/v [U-99% 2H] TFE, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] protein, 20 mM bis-TRIS, 0.175 v/v [U-99% 2H] TFE, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] protein, 20 mM bis-TRIS, 0.175 v/v [U-99% 2H] TFE, 100% D2O \| 100% D2O NMR sample composition 0.5 mM [U-99% 13C; U-99% 15N] protein, 0.5 mM protein, 20 mM bis-TRIS, 0.175 v/v [U-99% 2H] TFE, 100% D2O \| 100% D2O	Resolution not provided
2MAK Solution structure of the STIM1 CC1-CC2 homodimer in complex with two Orai1 C-terminal domains. Deposited 2013-07-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 312–387（76 aa） Fragment：UNP residues 312-387 Chain C 312–387（76 aa） Fragment：UNP residues 312-387	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；308 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition 0.25 mM [U-100% 15N] protein_1, 3.0 mM protein_2, 20 mM bis-TRIS, 0.175 v/v [U-99% 2H] TFE, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.25 mM [U-99% 13C; U-99% 15N] protein_1, 3.0 mM protein_2, 20 mM bis-TRIS, 0.175 v/v [U-99% 2H] TFE, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.25 mM [U-99% 13C; U-99% 15N] protein_1, 3.0 mM protein_2, 20 mM bis-TRIS, 0.175 v/v [U-99% 2H] TFE, 100% D2O \| 100% D2O NMR sample composition 2.5 mM protein_1, 0.25 mM [U-99% 15N] protein_2, 20 mM bis-TRIS, 0.175 v/v [U-99% 2H] TFE, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2.5 mM protein_1, 0.25 mM [U-99% 13C; U-99% 15N] protein_2, 20 mM bis-TRIS, 0.175 v/v [U-99% 2H] TFE, 100% D2O \| 100% D2O	Resolution not provided
3TEQ Crystal structure of SOAR domain Deposited 2011-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 344–444（101 aa） Fragment：SOAR domain (UNP RESIDUES 344-444) Chain C 344–444（101 aa） Fragment：SOAR domain (UNP RESIDUES 344-444)	Mutation：L374M, V419A, C437T Mutation：L374M, V419A, C437T	PO4 PHOSPHATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1M Bis-Tris pH 6.5, 10% PEG3350, 0.2M Ammonium dibasic phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.90 Å R-free 0.249
3TEQ Crystal structure of SOAR domain Deposited 2011-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 344–444（101 aa） Fragment：SOAR domain (UNP RESIDUES 344-444)	Mutation：L374M, V419A, C437T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1M Bis-Tris pH 6.5, 10% PEG3350, 0.2M Ammonium dibasic phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.90 Å R-free 0.249
3TEQ Crystal structure of SOAR domain Deposited 2011-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 344–444（101 aa） Fragment：SOAR domain (UNP RESIDUES 344-444)	Mutation：L374M, V419A, C437T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1M Bis-Tris pH 6.5, 10% PEG3350, 0.2M Ammonium dibasic phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.90 Å R-free 0.249
4O9B The Structure of CC1-IH in human STIM1. Deposited 2014-01-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 237–340（104 aa） Fragment：CC1-IH, UNP RESIDUES 237-340 Chain D 237–340（104 aa） Fragment：CC1-IH, UNP RESIDUES 237-340	Mutation：M244L, L321M Mutation：M244L, L321M	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；24% PEGMME 2000, 0.1M sodium acetate, 0.02M magnesium chloride hexahydrate, 0.02M nickel chloride hexahydrate, 0.02M cadmium chloride hexahydrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.289
4O9B The Structure of CC1-IH in human STIM1. Deposited 2014-01-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 237–340（104 aa） Fragment：CC1-IH, UNP RESIDUES 237-340 Chain C 237–340（104 aa） Fragment：CC1-IH, UNP RESIDUES 237-340	Mutation：M244L, L321M Mutation：M244L, L321M	CD CADMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；24% PEGMME 2000, 0.1M sodium acetate, 0.02M magnesium chloride hexahydrate, 0.02M nickel chloride hexahydrate, 0.02M cadmium chloride hexahydrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.289
4O9B The Structure of CC1-IH in human STIM1. Deposited 2014-01-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 237–340（104 aa） Fragment：CC1-IH, UNP RESIDUES 237-340 Chain B 237–340（104 aa） Fragment：CC1-IH, UNP RESIDUES 237-340	Mutation：M244L, L321M Mutation：M244L, L321M	CD CADMIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；24% PEGMME 2000, 0.1M sodium acetate, 0.02M magnesium chloride hexahydrate, 0.02M nickel chloride hexahydrate, 0.02M cadmium chloride hexahydrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.289
4O9B The Structure of CC1-IH in human STIM1. Deposited 2014-01-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 237–340（104 aa） Fragment：CC1-IH, UNP RESIDUES 237-340 Chain D 237–340（104 aa） Fragment：CC1-IH, UNP RESIDUES 237-340	Mutation：M244L, L321M Mutation：M244L, L321M	CD CADMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；24% PEGMME 2000, 0.1M sodium acetate, 0.02M magnesium chloride hexahydrate, 0.02M nickel chloride hexahydrate, 0.02M cadmium chloride hexahydrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.289
4O9B The Structure of CC1-IH in human STIM1. Deposited 2014-01-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 237–340（104 aa） Fragment：CC1-IH, UNP RESIDUES 237-340 Chain B 237–340（104 aa） Fragment：CC1-IH, UNP RESIDUES 237-340 Chain C 237–340（104 aa） Fragment：CC1-IH, UNP RESIDUES 237-340 Chain D 237–340（104 aa） Fragment：CC1-IH, UNP RESIDUES 237-340	Mutation：M244L, L321M Mutation：M244L, L321M Mutation：M244L, L321M Mutation：M244L, L321M	CD CADMIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；24% PEGMME 2000, 0.1M sodium acetate, 0.02M magnesium chloride hexahydrate, 0.02M nickel chloride hexahydrate, 0.02M cadmium chloride hexahydrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.289
6YEL Stromal interaction molecule 1 coiled-coil 1 fragment Deposited 2020-03-25	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 234–343（110 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.25；310.15 K；Ionic strength (raw mmCIF value) 0.02；Pressure 1 NMR sample composition 0.3 mM [U-98% 13C; U-98% 15N] STIM1 CC1, 20 mM TRIS, 7 mM [U-13C] SDS, 90 % v/v H2O, 10 % v/v [U-99% 2H] H2O, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

5 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STIM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–150； UniProt 58–201

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	2k60
Deposition date deposition_date	2008-07-02
Structure title title	NMR structure of calcium-loaded STIM1 EF-SAM
Keywords keywords	;EF-hand, SAM domain, EF-SAM, STIM1, stromal interaction molecule, store operated calcium entry regulator, SOCE, endoplasmic reticulum luminal calcium sensor, Calcium transport, Glycoprotein, Ion transport, Membrane, Phosphoprotein, Transmembrane, Transport, TRANSPORT PROTEIN, SIGNALING PROTEIN ;; SIGNALING 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	15.21 Å
Radius of gyration Rg (electron density) rg_electron	14.90 Å
Forward intensity I(0) i0	1733960000.00
Molecular weight molecular_weight	347370.0 kDa
Excluded volume excluded_volume	431040 Å³
Envelope volume envelope_volume	33691 Å³
Hydration-shell volume shell_volume	17031 Å³
Envelope diameter envelope_diameter	55.2 Å
Shell Rg shell_rg	22.67 Å
Envelope Rg envelope_rg	16.57 Å
Shape Rg shape_rg	14.88 Å
Total Rg total_rg	15.05 Å
Total atoms total_atoms	47920
Residues n_residues	3000
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	50.5 Å
Rg (real space) rg_real	15.12 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	1.7340e+09
I(0) uncertainty (real space) i0_real_error	1.7960e+07
Rg (reciprocal space) rg_reciprocal	15.13 Å
I(0) (reciprocal space) i0_reciprocal	1734000000.0000
Solution quality estimate total_estimate	0.8026
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.2 Å
Skewness Skewness skewness	0.150
Kurtosis Kurtosis kurtosis	-0.342
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	528100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; 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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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2k60A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	180 —

Domain ID domain_id	2k60A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Description description	PROTEIN (Stromal interaction molecule 1)
Molecular weight formula_weight	17380.4 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	47920

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

NMR structure of calcium-loaded STIM1 EF-SAM

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

PROTEIN (Stromal interaction molecule 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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/k6/2k60/2k60.fit
pddf	/app/data/pr_computation/k6/2k60/2k60.pr.out
profile	/app/data/saxs_computation/k6/2k60/2k60.dat