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- PDB-5l0p: Symmetry-based assembly of a two-dimensional protein lattice -

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Basic information

Entry
Database: PDB / ID: 5l0p
TitleSymmetry-based assembly of a two-dimensional protein lattice
ComponentsTranscription factor ETV6, Transcription factor ETV6, Transcription factor ETV6, Ferric uptake regulation protein chimera
KeywordsDE NOVO PROTEIN / design / lattice / 2D / assembly
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / Signaling by FLT3 fusion proteins / neurogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / ETS family / Ets-domain signature 2. / Ets domain ...Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcription factor ETV6 / Ferric uptake regulation protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Klebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFaham, S.
CitationJournal: PLoS ONE / Year: 2017
Title: Symmetry based assembly of a 2 dimensional protein lattice.
Authors: Poulos, S. / Agah, S. / Jallah, N. / Faham, S.
History
DepositionJul 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Category: refine
Item: _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work
Revision 1.3Oct 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription factor ETV6, Transcription factor ETV6, Transcription factor ETV6, Ferric uptake regulation protein chimera


Theoretical massNumber of molelcules
Total (without water)40,5601
Polymers40,5601
Non-polymers00
Water2,162120
1
A: Transcription factor ETV6, Transcription factor ETV6, Transcription factor ETV6, Ferric uptake regulation protein chimera

A: Transcription factor ETV6, Transcription factor ETV6, Transcription factor ETV6, Ferric uptake regulation protein chimera


Theoretical massNumber of molelcules
Total (without water)81,1192
Polymers81,1192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area2490 Å2
ΔGint-14 kcal/mol
Surface area31610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.313, 54.833, 88.480
Angle α, β, γ (deg.)90.00, 128.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcription factor ETV6, Transcription factor ETV6, Transcription factor ETV6, Ferric uptake regulation protein chimera / ETS translocation variant 6 / ETS-related protein Tel1 / Tel / Ferric uptake regulator


Mass: 40559.727 Da / Num. of mol.: 1
Fragment: 3 x TelSAM (UNP residues 47-124) + FUR (UNP residues 3-83) with connecting linkers
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: ETV6, TEL, TEL1, fur / Production host: Escherichia coli (E. coli) / References: UniProt: P41212, UniProt: P45599
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris, pH 8.0, 3.5 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20782 / % possible obs: 93.9 % / Redundancy: 4.8 % / Net I/σ(I): 15.9
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.283

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Processing

Software
NameClassification
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1JI7 & 2FU4

1ji7

2fu4


Resolution: 2.3→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2356 --
Rwork0.1982 --
obs-19724 93.9 %
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2537 0 0 120 2657
LS refinement shellResolution: 2.3→2.36 Å /
RfactorNum. reflection
Rfree0.319 57
Rwork0.24 -
obs-1065

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