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- PDB-6c4u: Engineered FHA with Myc-pTBD peptide -

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Basic information

Entry
Database: PDB / ID: 6c4u
TitleEngineered FHA with Myc-pTBD peptide
Components
  • Forkhead-associated 1
  • Myc-pTBD peptide
KeywordsPEPTIDE BINDING PROTEIN / FHA / Protein Engineering / Myc pT58 target
Function / homology
Function and homology information


SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / deoxyribonucleoside triphosphate biosynthetic process / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / RNA polymerase II transcription repressor complex / regulation of cell cycle process / regulation of somatic stem cell population maintenance / Binding of TCF/LEF:CTNNB1 to target gene promoters / meiotic recombination checkpoint signaling ...SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / deoxyribonucleoside triphosphate biosynthetic process / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / RNA polymerase II transcription repressor complex / regulation of cell cycle process / regulation of somatic stem cell population maintenance / Binding of TCF/LEF:CTNNB1 to target gene promoters / meiotic recombination checkpoint signaling / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of cell division / negative regulation of monocyte differentiation / negative regulation of phosphorylation / transcription regulator activator activity / Transcription of E2F targets under negative control by DREAM complex / response to growth factor / dual-specificity kinase / regulation of telomere maintenance / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / positive regulation of mesenchymal cell proliferation / protein-DNA complex disassembly / negative regulation of gene expression via chromosomal CpG island methylation / calcium/calmodulin-dependent protein kinase activity / branching involved in ureteric bud morphogenesis / Signaling by ALK / E-box binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / DNA replication origin binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / negative regulation of DNA damage checkpoint / DNA replication initiation / chromosome organization / regulation of DNA repair / Cyclin E associated events during G1/S transition / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of fibroblast proliferation / : / ERK1 and ERK2 cascade / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / transcription coregulator binding / positive regulation of epithelial cell proliferation / response to gamma radiation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / MAPK6/MAPK4 signaling / protein localization / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / cellular response to UV / MAPK cascade / positive regulation of fibroblast proliferation / cellular response to xenobiotic stimulus / cellular response to oxidative stress / cellular response to hypoxia / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / intracellular iron ion homeostasis / Estrogen-dependent gene expression / protein dimerization activity / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / protein kinase activity / chromatin remodeling / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / positive regulation of cell population proliferation / protein-containing complex binding / positive regulation of gene expression / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / Myc amino-terminal region / Serine/threonine-protein kinase Rad53 / Tumour Suppressor Smad4 - #20 / Helix-loop-helix DNA-binding domain / Tumour Suppressor Smad4 / Forkhead associated domain ...Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / Myc amino-terminal region / Serine/threonine-protein kinase Rad53 / Tumour Suppressor Smad4 - #20 / Helix-loop-helix DNA-binding domain / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Myc proto-oncogene protein / Serine/threonine-protein kinase RAD53
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKall, S.L. / Lavie, A.
CitationJournal: N Biotechnol / Year: 2018
Title: Generating a recombinant phosphothreonine-binding domain for a phosphopeptide of the human transcription factor, c-Myc.
Authors: Venegas, L.A. / Kall, S.L. / Bankole, O. / Lavie, A. / Kay, B.K.
History
DepositionJan 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Forkhead-associated 1
C: Forkhead-associated 1
D: Forkhead-associated 1
E: Forkhead-associated 1
A: Forkhead-associated 1
F: Forkhead-associated 1
G: Myc-pTBD peptide
I: Myc-pTBD peptide
H: Myc-pTBD peptide
J: Myc-pTBD peptide
L: Myc-pTBD peptide
K: Myc-pTBD peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,17413
Polymers97,08212
Non-polymers921
Water1,20767
1
F: Forkhead-associated 1
L: Myc-pTBD peptide


Theoretical massNumber of molelcules
Total (without water)16,1802
Polymers16,1802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Forkhead-associated 1
H: Myc-pTBD peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2723
Polymers16,1802
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-7 kcal/mol
Surface area7690 Å2
MethodPISA
3
C: Forkhead-associated 1
I: Myc-pTBD peptide


Theoretical massNumber of molelcules
Total (without water)16,1802
Polymers16,1802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-7 kcal/mol
Surface area7460 Å2
MethodPISA
4
D: Forkhead-associated 1
J: Myc-pTBD peptide


Theoretical massNumber of molelcules
Total (without water)16,1802
Polymers16,1802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-7 kcal/mol
Surface area7370 Å2
MethodPISA
5
E: Forkhead-associated 1
K: Myc-pTBD peptide


Theoretical massNumber of molelcules
Total (without water)16,1802
Polymers16,1802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-7 kcal/mol
Surface area7690 Å2
MethodPISA
6
A: Forkhead-associated 1
G: Myc-pTBD peptide


Theoretical massNumber of molelcules
Total (without water)16,1802
Polymers16,1802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-7 kcal/mol
Surface area7550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.180, 72.370, 280.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11L-101-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
12B
22D
13B
23E
14B
24A
15B
25F
16C
26D
17C
27E
18C
28A
19C
29F
110D
210E
111D
211A
112D
212F
113E
213A
114E
214F
115A
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLEULEUBA31 - 1553 - 127
21ASNASNLEULEUCB31 - 1553 - 127
12GLUGLUSERSERBA30 - 1542 - 126
22GLUGLUSERSERDC30 - 1542 - 126
13ASNASNLEULEUBA31 - 1553 - 127
23ASNASNLEULEUED31 - 1553 - 127
14GLUGLULEULEUBA30 - 1552 - 127
24GLUGLULEULEUAE30 - 1552 - 127
15ASNASNLEULEUBA31 - 1553 - 127
25ASNASNLEULEUFF31 - 1553 - 127
16ASNASNSERSERCB31 - 1543 - 126
26ASNASNSERSERDC31 - 1543 - 126
17ASNASNGLNGLNCB31 - 1573 - 129
27ASNASNGLNGLNED31 - 1573 - 129
18ASNASNLEULEUCB31 - 1553 - 127
28ASNASNLEULEUAE31 - 1553 - 127
19ASNASNLEULEUCB31 - 1553 - 127
29ASNASNLEULEUFF31 - 1553 - 127
110ASNASNSERSERDC31 - 1543 - 126
210ASNASNSERSERED31 - 1543 - 126
111GLUGLUSERSERDC30 - 1542 - 126
211GLUGLUSERSERAE30 - 1542 - 126
112ASNASNSERSERDC31 - 1543 - 126
212ASNASNSERSERFF31 - 1543 - 126
113ASNASNLEULEUED31 - 1553 - 127
213ASNASNLEULEUAE31 - 1553 - 127
114ASNASNLEULEUED31 - 1553 - 127
214ASNASNLEULEUFF31 - 1553 - 127
115ASNASNLEULEUAE31 - 1553 - 127
215ASNASNLEULEUFF31 - 1553 - 127

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Forkhead-associated 1


Mass: 15134.141 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P22216*PLUS
#2: Protein/peptide
Myc-pTBD peptide


Mass: 1046.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01106*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.69 Å3/Da / Density % sol: 66.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.4 M Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→140.18 Å / Num. obs: 47879 / % possible obs: 98.4 % / Redundancy: 6.96 % / CC1/2: 0.99 / Rrim(I) all: 0.069 / Net I/av σ(I): 16.08 / Net I/σ(I): 16.08
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5.78 % / Mean I/σ(I) obs: 1.17 / CC1/2: 0.867 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOLREPphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1g6g

1g6g


Resolution: 2.6→140.18 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 24.505 / SU ML: 0.41 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2791 2140 4.9 %RANDOM
Rwork0.23274 ---
obs0.2349 41567 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.442 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å20 Å20 Å2
2--10.91 Å20 Å2
3----8.96 Å2
Refinement stepCycle: 1 / Resolution: 2.6→140.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6408 0 6 67 6481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196527
X-RAY DIFFRACTIONr_bond_other_d0.0020.026195
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9818858
X-RAY DIFFRACTIONr_angle_other_deg0.994314443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2215795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.53825.385286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.076151172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.141530
X-RAY DIFFRACTIONr_chiral_restr0.1040.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217037
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021197
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_it7.6169.3423216
X-RAY DIFFRACTIONr_mcbond_other7.6169.3423215
X-RAY DIFFRACTIONr_mcangle_it11.48713.9913999
X-RAY DIFFRACTIONr_mcangle_other11.48513.9914000
X-RAY DIFFRACTIONr_scbond_it7.8089.8283311
X-RAY DIFFRACTIONr_scbond_other7.8069.8293311
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.97214.5014859
X-RAY DIFFRACTIONr_long_range_B_refined16.0636881
X-RAY DIFFRACTIONr_long_range_B_other16.0596881
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B75440.1
12C75440.1
21B75000.1
22D75000.1
31B75900.1
32E75900.1
41B76040.1
42A76040.1
51B75660.09
52F75660.09
61C75020.1
62D75020.1
71C78640.08
72E78640.08
81C76100.09
82A76100.09
91C74540.1
92F74540.1
101D75180.1
102E75180.1
111D75240.1
112A75240.1
121D73540.1
122F73540.1
131E76960.08
132A76960.08
141E75260.1
142F75260.1
151A75280.1
152F75280.1
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.521 133 -
Rwork0.509 3087 -
obs--99.72 %

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