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- PDB-9b8u: Crystal structure of CRX-Ret4 oligonucleotide complex -

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Basic information

Entry
Database: PDB / ID: 9b8u
TitleCrystal structure of CRX-Ret4 oligonucleotide complex
Components
  • Cone-rod homeobox protein
  • DNA (5'-D(P*CP*AP*GP*GP*AP*GP*CP*TP*TP*AP*GP*GP*AP*GP*GP*GP*GP*GP*AP*G)-3')
  • DNA (5'-D(P*CP*TP*CP*CP*CP*CP*CP*TP*CP*CP*TP*AP*AP*GP*CP*TP*CP*CP*TP*G)-3')
KeywordsTRANSCRIPTION/DNA / Homeodomain / Transcription factor / vision / rhodopsin promoter / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


leucine zipper domain binding / DNA-binding transcription activator activity / visual perception / animal organ morphogenesis / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific ...leucine zipper domain binding / DNA-binding transcription activator activity / visual perception / animal organ morphogenesis / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RNA polymerase II transcription regulator complex / sequence-specific double-stranded DNA binding / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Transcription factor Otx, C-terminal / Otx1 transcription factor / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
CACODYLATE ION / : / DNA / DNA (> 10) / Cone-rod homeobox protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSrivastava, D. / Artemyev, N.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)1R01EY034455-01 United States
CitationJournal: Structure / Year: 2024
Title: Molecular basis of CRX/DNA recognition and stoichiometry at the Ret4 response element.
Authors: Srivastava, D. / Gowribidanur-Chinnaswamy, P. / Gaur, P. / Spies, M. / Swaroop, A. / Artemyev, N.O.
History
DepositionApr 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cone-rod homeobox protein
B: Cone-rod homeobox protein
C: Cone-rod homeobox protein
D: Cone-rod homeobox protein
E: DNA (5'-D(P*CP*AP*GP*GP*AP*GP*CP*TP*TP*AP*GP*GP*AP*GP*GP*GP*GP*GP*AP*G)-3')
F: DNA (5'-D(P*CP*TP*CP*CP*CP*CP*CP*TP*CP*CP*TP*AP*AP*GP*CP*TP*CP*CP*TP*G)-3')
G: DNA (5'-D(P*CP*AP*GP*GP*AP*GP*CP*TP*TP*AP*GP*GP*AP*GP*GP*GP*GP*GP*AP*G)-3')
H: DNA (5'-D(P*CP*TP*CP*CP*CP*CP*CP*TP*CP*CP*TP*AP*AP*GP*CP*TP*CP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,74320
Polymers64,8198
Non-polymers92412
Water99155
1
A: Cone-rod homeobox protein
B: Cone-rod homeobox protein
E: DNA (5'-D(P*CP*AP*GP*GP*AP*GP*CP*TP*TP*AP*GP*GP*AP*GP*GP*GP*GP*GP*AP*G)-3')
F: DNA (5'-D(P*CP*TP*CP*CP*CP*CP*CP*TP*CP*CP*TP*AP*AP*GP*CP*TP*CP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,06411
Polymers32,4094
Non-polymers6557
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-21 kcal/mol
Surface area14450 Å2
MethodPISA
2
C: Cone-rod homeobox protein
D: Cone-rod homeobox protein
G: DNA (5'-D(P*CP*AP*GP*GP*AP*GP*CP*TP*TP*AP*GP*GP*AP*GP*GP*GP*GP*GP*AP*G)-3')
H: DNA (5'-D(P*CP*TP*CP*CP*CP*CP*CP*TP*CP*CP*TP*AP*AP*GP*CP*TP*CP*CP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6799
Polymers32,4094
Non-polymers2695
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-44 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.597, 75.494, 97.229
Angle α, β, γ (deg.)90.000, 120.248, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cone-rod homeobox protein


Mass: 9780.068 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRX, CORD2 / Production host: Escherichia coli (E. coli) / References: UniProt: O43186

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DNA chain , 2 types, 4 molecules EGFH

#2: DNA chain DNA (5'-D(P*CP*AP*GP*GP*AP*GP*CP*TP*TP*AP*GP*GP*AP*GP*GP*GP*GP*GP*AP*G)-3')


Mass: 6618.272 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*CP*TP*CP*CP*CP*CP*CP*TP*CP*CP*TP*AP*AP*GP*CP*TP*CP*CP*TP*G)-3')


Mass: 6231.013 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 6 types, 67 molecules

#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 80 mM KCl, 40 mM cacodylate pH 6.0, 55% MPD, 12 mM Spermine tetrahydrochloride
PH range: 6.o-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→57.4 Å / Num. obs: 15350 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 75.18 Å2 / CC1/2: 0.952 / Rmerge(I) obs: 0.265 / Rpim(I) all: 0.112 / Rrim(I) all: 0.289 / Net I/σ(I): 9.5
Reflection shellResolution: 2.9→3.12 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2466 / CC1/2: 0.869 / Rpim(I) all: 0.389 / Rrim(I) all: 1.051 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→54.67 Å / SU ML: 0.4646 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.0951
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2492 746 9.98 %
Rwork0.2492 13733 -
obs0.253 15256 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.34 Å2
Refinement stepCycle: LAST / Resolution: 2.9→54.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 1640 47 55 3878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344048
X-RAY DIFFRACTIONf_angle_d0.56295786
X-RAY DIFFRACTIONf_chiral_restr0.0309630
X-RAY DIFFRACTIONf_plane_restr0.0038467
X-RAY DIFFRACTIONf_dihedral_angle_d22.74141731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.40571260.30821214X-RAY DIFFRACTION98.31
2.99-3.10.32861370.30111238X-RAY DIFFRACTION100
3.1-3.220.34471470.27431254X-RAY DIFFRACTION100
3.22-3.370.33321410.22871239X-RAY DIFFRACTION99.64
3.37-3.550.28711370.22851249X-RAY DIFFRACTION100
3.55-3.770.30551310.24631248X-RAY DIFFRACTION99.86
3.77-4.060.3111380.23781258X-RAY DIFFRACTION99.36
4.06-4.470.28381410.22671231X-RAY DIFFRACTION98.42
4.47-5.120.25241440.24441274X-RAY DIFFRACTION99.93
5.12-6.440.3041350.2711245X-RAY DIFFRACTION99.42
6.45-54.670.2421460.251283X-RAY DIFFRACTION98.96
Refinement TLS params.Method: refined / Origin x: 34.4241604531 Å / Origin y: -35.6416699061 Å / Origin z: -23.7659494485 Å
111213212223313233
T0.489691423062 Å2-0.00753694524377 Å20.00632530259153 Å2-0.429607318501 Å20.0073257296278 Å2--0.455230669317 Å2
L0.428165027483 °2-0.507842901199 °2-0.427500081088 °2-0.0278944741128 °20.807404488457 °2--0.594402437163 °2
S0.0232280040758 Å °0.0512730103587 Å °-0.0720269657922 Å °-0.0329903186479 Å °-0.0796449827691 Å °0.0109379613143 Å °-0.0761516851597 Å °-0.0783682363149 Å °-0.00141920902511 Å °
Refinement TLS groupSelection details: all

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