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- PDB-4yoz: p107 pocket domain in complex with HPV E7 peptide -

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Basic information

Entry
Database: PDB / ID: 4yoz
Titlep107 pocket domain in complex with HPV E7 peptide
Components
  • HPV E7 peptide
  • Retinoblastoma-like protein 1,Retinoblastoma-like protein 1
KeywordsTRANSCRIPTION / Pocket protein / Cyclin Box / Transcriptional regulator / Cell Cycle
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated activation of of host transcription / : / regulation of lipid kinase activity / : / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / G1/S-Specific Transcription ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated activation of of host transcription / : / regulation of lipid kinase activity / : / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / G1/S-Specific Transcription / cadmium ion binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of cellular senescence / G0 and Early G1 / viral process / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Cyclin D associated events in G1 / chromatin organization / DNA-binding transcription factor binding / host cell cytoplasm / transcription regulator complex / cell differentiation / cell cycle / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of gene expression / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm
Similarity search - Function
Papillomavirus E7 / E7 protein, Early protein / Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain ...Papillomavirus E7 / E7 protein, Early protein / Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) / Retinoblastoma-associated protein A domain / Rb C-terminal domain / Cyclin-like / Cyclin A; domain 1 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein E7 / Retinoblastoma-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.245 Å
AuthorsLiban, T.J. / Guiley, K.Z. / Felthousen, J.G. / Ramanan, P. / Litovchick, L. / Rubin, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA132685 United States
CitationJournal: Genes Dev. / Year: 2015
Title: Structural mechanisms of DREAM complex assembly and regulation.
Authors: Guiley, K.Z. / Liban, T.J. / Felthousen, J.G. / Ramanan, P. / Litovchick, L. / Rubin, S.M.
History
DepositionMar 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Other
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Retinoblastoma-like protein 1,Retinoblastoma-like protein 1
B: HPV E7 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8106
Polymers44,4262
Non-polymers3844
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-60 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.690, 76.550, 74.680
Angle α, β, γ (deg.)90.00, 120.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1186-

HOH

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Components

#1: Protein Retinoblastoma-like protein 1,Retinoblastoma-like protein 1 / 107 kDa retinoblastoma-associated protein / p107 / pRb1


Mass: 43265.965 Da / Num. of mol.: 1 / Fragment: unp residues 391-593,unp residues 391-593
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBL1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P28749
#2: Protein/peptide HPV E7 peptide


Mass: 1160.255 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P03129*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Hepes, Ammonium Sulfate, PEG 400

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.2→57.2 Å / Num. all: 21552 / Num. obs: 21552 / % possible obs: 93.2 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.6
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Cootmodel building
Blu-Icedata collection
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.245→57.195 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 2000 9.28 %
Rwork0.1837 --
obs0.1888 21549 92.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.245→57.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2881 0 20 111 3012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052952
X-RAY DIFFRACTIONf_angle_d0.8733990
X-RAY DIFFRACTIONf_dihedral_angle_d13.7931097
X-RAY DIFFRACTIONf_chiral_restr0.033449
X-RAY DIFFRACTIONf_plane_restr0.004499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2451-2.30120.26171410.2181385X-RAY DIFFRACTION94
2.3012-2.36340.27671450.21011413X-RAY DIFFRACTION94
2.3634-2.4330.26161450.20451412X-RAY DIFFRACTION94
2.433-2.51150.23791420.18581398X-RAY DIFFRACTION94
2.5115-2.60130.23641450.18091420X-RAY DIFFRACTION94
2.6013-2.70540.23811430.17181389X-RAY DIFFRACTION93
2.7054-2.82860.23671430.17381400X-RAY DIFFRACTION93
2.8286-2.97770.22641450.18971415X-RAY DIFFRACTION93
2.9777-3.16420.29551430.19961392X-RAY DIFFRACTION93
3.1642-3.40850.26521420.19411392X-RAY DIFFRACTION93
3.4085-3.75150.23971430.17621392X-RAY DIFFRACTION92
3.7515-4.29420.19411410.161386X-RAY DIFFRACTION92
4.2942-5.40950.21951410.16891381X-RAY DIFFRACTION90
5.4095-57.21380.24831410.19741374X-RAY DIFFRACTION88
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)
12.6840.55650.14792.2978-0.46422.1273-0.03330.138-0.1063-0.24030.0993-0.36990.11340.1656-0.06350.16670.02470.0350.1722-0.0480.188121.282911.1822-7.4632
21.35040.0657-0.32620.9784-0.08820.9824-0.059-0.1137-0.13440.01720.0371-0.20030.03960.10740.02290.12370.0146-0.00850.1428-0.00150.148115.967311.90362.9397
33.92790.07522.46251.85470.90511.97920.1523-0.1986-0.45610.0468-0.2101-0.3450.78750.25270.06210.49410.01070.02910.41250.15030.253-1.0095.965418.7161
41.6811-0.0157-0.08422.15580.75722.4673-0.0751-0.60010.2780.46160.0188-0.1134-0.27890.03760.04820.30010.0282-0.03870.3472-0.09370.22955.070125.784625.9786
53.0469-3.00632.23096.93731.95325.9791-0.03320.12960.0971-0.1143-0.0737-0.25890.04740.37530.08410.4110.1062-0.07850.7452-0.37940.59830.828740.712430.0641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 389 through 453 )
2X-RAY DIFFRACTION2chain 'A' and (resid 454 through 580 )
3X-RAY DIFFRACTION3chain 'A' and (resid 581 through 784 )
4X-RAY DIFFRACTION4chain 'A' and (resid 785 through 967 )
5X-RAY DIFFRACTION5chain 'B' and (resid 21 through 29 )

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