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- PDB-5k8q: Crystal Structure of Calcium-loaded Calmodulin in complex with ST... -

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Basic information

Entry
Database: PDB / ID: 5k8q
TitleCrystal Structure of Calcium-loaded Calmodulin in complex with STRA6 CaMBP2-site peptide.
Components
  • Calmodulin
  • Zgc:136689
KeywordsMETAL BINDING PROTEIN / Calmodulin / STRA6 / peptide complex / unique fold
Function / homology
Function and homology information


vitamin A import into cell / The canonical retinoid cycle in rods (twilight vision) / retinol transport / retinol transmembrane transporter activity / chordate embryonic development / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / retinal binding / CaM pathway ...vitamin A import into cell / The canonical retinoid cycle in rods (twilight vision) / retinol transport / retinol transmembrane transporter activity / chordate embryonic development / : / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / retinal binding / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / regulation of synaptic vesicle endocytosis / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / retinol binding / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / positive regulation of cyclic-nucleotide phosphodiesterase activity / regulation of synaptic vesicle exocytosis / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / regulation of cardiac muscle cell action potential / Activation of RAC1 downstream of NMDARs / response to corticosterone / positive regulation of DNA binding / positive regulation of ryanodine-sensitive calcium-release channel activity / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / negative regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / plasma membrane => GO:0005886 / RHO GTPases activate PAKs / : / Ion transport by P-type ATPases / Long-term potentiation / Uptake and function of anthrax toxins / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / adenylate cyclase binding / catalytic complex / DARPP-32 events / detection of calcium ion / regulation of cardiac muscle contraction / regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / Protein methylation / phosphatidylinositol 3-kinase binding / eNOS activation / enzyme regulator activity / activation of adenylate cyclase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Activation of AMPK downstream of NMDARs / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / : / Ion homeostasis / titin binding / regulation of calcium-mediated signaling / positive regulation of protein autophosphorylation / voltage-gated potassium channel complex / sperm midpiece / calcium channel complex / response to amphetamine / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / nitric-oxide synthase regulator activity / regulation of heart rate / sarcomere / FCERI mediated Ca+2 mobilization / protein serine/threonine kinase activator activity / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / positive regulation of nitric-oxide synthase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / mitochondrial membrane / RAF activation
Similarity search - Function
Receptor for retinol uptake STRA6 / Retinol binding protein receptor / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
IMIDAZOLE / Receptor for retinol uptake stra6 / Calmodulin-1 / Calmodulin-3 / Receptor for retinol uptake stra6
Similarity search - Component
Biological speciesHomo sapiens (human)
Danio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.739 Å
AuthorsStowe, S.D. / Clarke, O.B. / Cavalier, M.C. / Godoy-Ruiz, R. / Mancia, F. / Weber, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM095315 United States
CitationJournal: Science / Year: 2016
Title: Structure of the STRA6 receptor for retinol uptake.
Authors: Yunting Chen / Oliver B Clarke / Jonathan Kim / Sean Stowe / Youn-Kyung Kim / Zahra Assur / Michael Cavalier / Raquel Godoy-Ruiz / Desiree C von Alpen / Chiara Manzini / William S Blaner / ...Authors: Yunting Chen / Oliver B Clarke / Jonathan Kim / Sean Stowe / Youn-Kyung Kim / Zahra Assur / Michael Cavalier / Raquel Godoy-Ruiz / Desiree C von Alpen / Chiara Manzini / William S Blaner / Joachim Frank / Loredana Quadro / David J Weber / Lawrence Shapiro / Wayne A Hendrickson / Filippo Mancia /
Abstract: Vitamin A homeostasis is critical to normal cellular function. Retinol-binding protein (RBP) is the sole specific carrier in the bloodstream for hydrophobic retinol, the main form in which vitamin A ...Vitamin A homeostasis is critical to normal cellular function. Retinol-binding protein (RBP) is the sole specific carrier in the bloodstream for hydrophobic retinol, the main form in which vitamin A is transported. The integral membrane receptor STRA6 mediates cellular uptake of vitamin A by recognizing RBP-retinol to trigger release and internalization of retinol. We present the structure of zebrafish STRA6 determined to 3.9-angstrom resolution by single-particle cryo-electron microscopy. STRA6 has one intramembrane and nine transmembrane helices in an intricate dimeric assembly. Unexpectedly, calmodulin is bound tightly to STRA6 in a noncanonical arrangement. Residues involved with RBP binding map to an archlike structure that covers a deep lipophilic cleft. This cleft is open to the membrane, suggesting a possible mode for internalization of retinol through direct diffusion into the lipid bilayer.
History
DepositionMay 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin
B: Zgc:136689
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1627
Polymers19,9332
Non-polymers2295
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-63 kcal/mol
Surface area9310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.510, 37.230, 35.730
Angle α, β, γ (deg.)90.00, 94.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-394-

HOH

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Components

#1: Protein Calmodulin / CaM


Mass: 16852.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide Zgc:136689


Mass: 3080.550 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized peptide with N-terminal acetylation and C-terminal amidation.
Source: (synth.) Danio rerio (zebrafish) / References: UniProt: Q1ECX5, UniProt: F1RAX4*PLUS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Imidazole pH 5.5, 28%(v/v) PEGMME 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.739→25.37 Å / Num. obs: 21134 / % possible obs: 98.8 % / Redundancy: 3.2 % / CC1/2: 0.986 / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.7
Reflection shellResolution: 1.739→1.801 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.2 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.10-2155refinement
iMOSFLM7.2.1data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IZUZ

Resolution: 1.739→25.368 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 28.36
RfactorNum. reflection% reflection
Rfree0.2673 1029 4.86 %
Rwork0.2271 --
obs0.2291 21134 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.739→25.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 9 130 1476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161418
X-RAY DIFFRACTIONf_angle_d0.8691867
X-RAY DIFFRACTIONf_dihedral_angle_d23.678854
X-RAY DIFFRACTIONf_chiral_restr0.052203
X-RAY DIFFRACTIONf_plane_restr0.005252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.739-1.78250.37871380.34172539X-RAY DIFFRACTION89
1.7825-1.83070.41591650.3452518X-RAY DIFFRACTION92
1.8307-1.88450.32891310.30612671X-RAY DIFFRACTION94
1.8845-1.94530.60491280.51172425X-RAY DIFFRACTION88
1.9453-2.01480.30161270.2722776X-RAY DIFFRACTION98
2.0148-2.09550.31341060.26592759X-RAY DIFFRACTION97
2.0955-2.19080.25931240.2152782X-RAY DIFFRACTION98
2.1908-2.30620.51171140.35382435X-RAY DIFFRACTION87
2.3062-2.45060.18531510.19052760X-RAY DIFFRACTION98
2.4506-2.63960.28811370.20022735X-RAY DIFFRACTION98
2.6396-2.90490.22461670.20162741X-RAY DIFFRACTION98
2.9049-3.32450.27641460.19672702X-RAY DIFFRACTION97
3.3245-4.18540.1711380.16932690X-RAY DIFFRACTION95
4.1854-25.37040.1941260.16712632X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.47-0.1399-1.48320.60340.15731.7222-0.0942-0.0693-0.0919-0.0045-0.0248-0.0990.07270.00350.0760.15210.01770.0090.15060.01110.0826.210810.600540.0373
24.7915-3.37-1.44762.37161.0980.95950.14160.2852-0.4512-0.2705-0.19550.3161-0.0119-0.2460.12270.1776-0.0068-0.02160.1180.03310.20921.44990.213428.3226
33.7561-0.8714-0.46412.84870.76721.7217-0.0262-0.1919-0.04910.15810.04460.21750.1145-0.04140.04290.11630.0113-0.00530.12250.06230.183428.4452-1.024136.4709
45.6058-1.5356-0.91783.38240.45314.6184-0.1846-0.5976-0.02170.3660.39890.44040.1151-0.12840.02810.10750.03520.02660.16440.0660.216120.72662.70436.932
52.1135-0.3477-0.01982.1996-1.5291.09360.1518-0.01810.7025-0.0797-0.1407-0.4461-0.7521-0.1234-0.11080.2874-0.0672-0.04570.2360.07530.412719.618716.481627.9963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 101 )
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 147 )
4X-RAY DIFFRACTION4chain 'B' and (resid 601 through 618 )
5X-RAY DIFFRACTION5chain 'B' and (resid 619 through 627 )

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