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- PDB-4htm: Mechanism of CREB Recognition and Coactivation by the CREB Regula... -

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Basic information

Entry
Database: PDB / ID: 4htm
TitleMechanism of CREB Recognition and Coactivation by the CREB Regulated Transcriptional Coactivator CRTC2
ComponentsCREB-regulated transcription coactivator 2
KeywordsPROTEIN BINDING / alpha-helix / CREB binding / CREB
Function / homology
Function and homology information


positive regulation of CREB transcription factor activity / cAMP response element binding protein binding / gluconeogenesis / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Circadian Clock / glucose homeostasis / protein homotetramerization / positive regulation of transcription by RNA polymerase II / extracellular exosome ...positive regulation of CREB transcription factor activity / cAMP response element binding protein binding / gluconeogenesis / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Circadian Clock / glucose homeostasis / protein homotetramerization / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transducer of regulated CREB activity, N-terminal / Transducer of regulated CREB activity, middle domain / Transducer of regulated CREB activity, C-terminal / CREB-regulated transcription coactivator / Transducer of regulated CREB activity, N terminus / Transducer of regulated CREB activity middle domain / Transducer of regulated CREB activity, C terminus
Similarity search - Domain/homology
CREB-regulated transcription coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLuo, Q. / Viste, K. / Urday-Zaa, J.C. / Kumar, G.S. / Tsai, W.-W. / Talai, A. / Mayo, K. / Montminy, M. / Radhakrishnan, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Protein kinase N1, a cell inhibitor of Akt kinase, has a central role in quality control of germinal center formation
Authors: Luo, Q. / Viste, K. / Urday-Zaa, J.C. / Kumar, G.S. / Tsai, W.-W. / Talai, A. / Mayo, K. / Montminy, M. / Radhakrishnan, I.
History
DepositionNov 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: CREB-regulated transcription coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1494
Polymers3,9521
Non-polymers1963
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CREB-regulated transcription coactivator 2
hetero molecules

A: CREB-regulated transcription coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2978
Polymers7,9052
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1340 Å2
ΔGint-241 kcal/mol
Surface area5370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)21.481, 57.631, 23.065
Angle α, β, γ (deg.)90.00, 94.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide CREB-regulated transcription coactivator 2 / Transducer of regulated cAMP response element-binding protein 2 / TORC-2 / Transducer of CREB protein 2


Mass: 3952.445 Da / Num. of mol.: 1 / Fragment: CRTC2 CREB binding domain: unp residues 18-50 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q53ET0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 1.8 Å3/Da / Density % sol: 31.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, 150 mM zinc acetate, 3 M NaCl and 12% ethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 76 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. all: 19070 / Num. obs: 2595 / % possible obs: 99.4 % / Rsym value: 0.087 / Net I/σ(I): 22.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 14.9 / Rsym value: 0.134 / % possible all: 100

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2→14.41 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.84 / SU B: 9.913 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28438 81 4.3 %RANDOM
Rwork0.24791 ---
obs0.24934 1817 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.317 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.03 Å2
2---0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2→14.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms231 0 3 27 261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.019232
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7071.959306
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.137527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.9425.38513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8911552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1.685152
X-RAY DIFFRACTIONr_chiral_restr0.0440.233
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.02168
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 9 -
Rwork0.329 125 -
obs--100 %
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)
119.772-3.62811.815529.17280.5570.986-0.29690.351.0205-0.1294-0.05810.60110.1560.46060.35510.06650.09040.0310.24240.13630.13483.344971.37427.0237
216.79555.2068-2.801427.67035.21928.55570.15950.1058-0.576-0.2520.0522-0.8110.4250.0983-0.21180.07640.00890.00630.0535-0.01850.05093.054661.81555.3083
30.7008-3.26991.192518.4021-1.03688.55470.00320.02480.0925-0.1432-0.007-0.5166-0.16370.18220.00390.034-0.00310.01930.05310.05320.09363.411951.60496.1766
419.21549.31046.36339.879.628116.5434-0.20760.7275-0.863-0.36520.1493-0.01080.03970.2480.05830.05070.023-0.01010.0475-0.04770.09223.031240.14384.928
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 11
2X-RAY DIFFRACTION2A12 - 16
3X-RAY DIFFRACTION3A17 - 25
4X-RAY DIFFRACTION4A26 - 31

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