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- PDB-4o9b: The Structure of CC1-IH in human STIM1. -

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Basic information

Entry
Database: PDB / ID: 4o9b
TitleThe Structure of CC1-IH in human STIM1.
ComponentsStromal interaction molecule 1
KeywordsSIGNALING PROTEIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / ALPHA HELICES / Signaling
Function / homology
Function and homology information


store-operated calcium entry / activation of store-operated calcium channel activity / regulation of store-operated calcium entry / cortical endoplasmic reticulum / enamel mineralization / Elevation of cytosolic Ca2+ levels / positive regulation of adenylate cyclase activity / microtubule plus-end binding / plasma membrane raft / regulation of calcium ion transport ...store-operated calcium entry / activation of store-operated calcium channel activity / regulation of store-operated calcium entry / cortical endoplasmic reticulum / enamel mineralization / Elevation of cytosolic Ca2+ levels / positive regulation of adenylate cyclase activity / microtubule plus-end binding / plasma membrane raft / regulation of calcium ion transport / detection of calcium ion / calcium channel regulator activity / Ion homeostasis / sarcoplasmic reticulum membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / intracellular calcium ion homeostasis / positive regulation of angiogenesis / protease binding / microtubule / calcium ion binding / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / plasma membrane
Similarity search - Function
Stromal interaction molecule 1, SAM domain / Stromal interaction molecule, Orai1-activating region / Stromal interaction molecule / STIM1 Orai1-activating region / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily ...Stromal interaction molecule 1, SAM domain / Stromal interaction molecule, Orai1-activating region / Stromal interaction molecule / STIM1 Orai1-activating region / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Stromal interaction molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.604 Å
AuthorsCui, B. / Yang, X. / Li, S. / Shen, Y.
CitationJournal: Plos One / Year: 2013
Title: The inhibitory helix controls the intramolecular conformational switching of the C-terminus of STIM1.
Authors: Cui, B. / Yang, X. / Li, S. / Lin, Z. / Wang, Z. / Dong, C. / Shen, Y.
History
DepositionJan 2, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionJan 15, 2014ID: 4IOZ
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stromal interaction molecule 1
B: Stromal interaction molecule 1
C: Stromal interaction molecule 1
D: Stromal interaction molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5387
Polymers50,2004
Non-polymers3373
Water1,11762
1
A: Stromal interaction molecule 1
D: Stromal interaction molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2133
Polymers25,1002
Non-polymers1121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-20 kcal/mol
Surface area15380 Å2
MethodPISA
2
B: Stromal interaction molecule 1
C: Stromal interaction molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3254
Polymers25,1002
Non-polymers2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-19 kcal/mol
Surface area15710 Å2
MethodPISA
3
A: Stromal interaction molecule 1

B: Stromal interaction molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2133
Polymers25,1002
Non-polymers1121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-y+1,x-y+1,z-1/31
Buried area2330 Å2
ΔGint-20 kcal/mol
Surface area15090 Å2
MethodPISA
4
D: Stromal interaction molecule 1
hetero molecules

C: Stromal interaction molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3254
Polymers25,1002
Non-polymers2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_445x-y-1,-y-1,-z+1/31
Buried area2570 Å2
ΔGint-18 kcal/mol
Surface area15060 Å2
MethodPISA
5
C: Stromal interaction molecule 1
hetero molecules

B: Stromal interaction molecule 1
hetero molecules

A: Stromal interaction molecule 1
D: Stromal interaction molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5387
Polymers50,2004
Non-polymers3373
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_664-y+1,x-y+1,z-1/31
crystal symmetry operation5_445x-y-1,-y-1,-z+1/31
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-45 kcal/mol
Surface area30590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.852, 101.852, 104.565
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11D-503-

HOH

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Components

#1: Protein
Stromal interaction molecule 1


Mass: 12550.119 Da / Num. of mol.: 4 / Fragment: CC1-IH, UNP RESIDUES 237-340 / Mutation: M244L, L321M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GOK, STIM1, STIM1 / Plasmid: pET-M / Production host: Escherichia coli (E. coli) / Strain (production host): Codon Plus / References: UniProt: Q13586
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 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

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2012
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 19528 / Num. obs: 17510 / % possible obs: 89.67 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.5 %
Reflection shellHighest resolution: 2.6 Å / Redundancy: 10.5 % / Num. unique all: 19528 / % possible all: 89.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.604→33.711 Å / SU ML: 0.41 / σ(F): 0 / Phase error: 31.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2892 907 5.18 %RANDOM
Rwork0.2279 ---
all0.247 19528 --
obs0.2311 17510 89.22 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.176 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.3188 Å2-0 Å20 Å2
2---9.3188 Å2-0 Å2
3---1.8375 Å2
Refinement stepCycle: LAST / Resolution: 2.604→33.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 3 62 2920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092869
X-RAY DIFFRACTIONf_angle_d1.1193828
X-RAY DIFFRACTIONf_dihedral_angle_d20.0731146
X-RAY DIFFRACTIONf_chiral_restr0.074424
X-RAY DIFFRACTIONf_plane_restr0.003517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6037-2.76670.36931080.28551850X-RAY DIFFRACTION61
2.7667-2.98020.3471360.26232456X-RAY DIFFRACTION80
2.9802-3.27990.341490.25672980X-RAY DIFFRACTION97
3.2799-3.7540.31991770.22923073X-RAY DIFFRACTION99
3.754-4.72750.25771710.18623096X-RAY DIFFRACTION100
4.7275-33.71370.24621660.2293148X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -19.069 Å / Origin y: 3.601 Å / Origin z: 14.03 Å
111213212223313233
T0.3877 Å2-0.0514 Å20.0009 Å2--0.0821 Å20.0376 Å2--0.1673 Å2
L0.3417 °20.0599 °2-0.006 °2-0.3679 °2-0.0422 °2--0.266 °2
S-0.1117 Å °0.0374 Å °0.1638 Å °0.1117 Å °0.2958 Å °0.1263 Å °-0.0725 Å °0.0456 Å °-0.0833 Å °
Refinement TLS groupSelection details: all

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