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- PDB-9lyv: structure of prrx bound to DNA -

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Basic information

Entry
Database: PDB / ID: 9lyv
Titlestructure of prrx bound to DNA
Components
  • DNA (5'-D(*TP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*A)-3')
  • Paired mesoderm homeobox protein 2
KeywordsDNA BINDING PROTEIN / DNA binding
Function / homology
Function and homology information


sequence-specific double-stranded DNA binding / 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 transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / nucleus
Similarity search - Function
Paired mesoderm homeobox protein 1/2 / OAR domain / OAR motif / OAR domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Paired mesoderm homeobox protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsDong, C. / Yan, X.J. / Guo, S.M. / Huang, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82473144 China
CitationJournal: Circ Res / Year: 2026
Title: Differential Impact of Recruited and Resident Macrophages on Hypoxia-Induced Pulmonary Hypertension.
Authors: Guo, S. / Pan, T. / Yan, X. / Cheng, Y. / Du, R. / Liu, Q. / Huang, Y. / Zhuo, Y. / Zhao, Y. / Tian, D. / Shi, X. / Qiang, T. / Cao, X. / Tang, X. / Korinek, V. / Huang, D. / Zhou, B. / ...Authors: Guo, S. / Pan, T. / Yan, X. / Cheng, Y. / Du, R. / Liu, Q. / Huang, Y. / Zhuo, Y. / Zhao, Y. / Tian, D. / Shi, X. / Qiang, T. / Cao, X. / Tang, X. / Korinek, V. / Huang, D. / Zhou, B. / Wang, J.W. / Dong, C. / Qi, Y. / Shen, Y. / Yu, Y.
History
DepositionFeb 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Paired mesoderm homeobox protein 2
B: DNA (5'-D(*TP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*A)-3')
C: DNA (5'-D(*TP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*A)-3')
D: Paired mesoderm homeobox protein 2
E: DNA (5'-D(*TP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*A)-3')
F: DNA (5'-D(*TP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*A)-3')
G: Paired mesoderm homeobox protein 2
H: DNA (5'-D(*TP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*A)-3')
I: DNA (5'-D(*TP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)44,5759
Polymers44,5759
Non-polymers00
Water7,999444
1
A: Paired mesoderm homeobox protein 2
B: DNA (5'-D(*TP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*A)-3')
C: DNA (5'-D(*TP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)14,8583
Polymers14,8583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Paired mesoderm homeobox protein 2
E: DNA (5'-D(*TP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*A)-3')
F: DNA (5'-D(*TP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)14,8583
Polymers14,8583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Paired mesoderm homeobox protein 2
H: DNA (5'-D(*TP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*A)-3')
I: DNA (5'-D(*TP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)14,8583
Polymers14,8583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.900, 96.900, 39.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Paired mesoderm homeobox protein 2 / Paired-related homeobox protein 2 / PRX-2


Mass: 7537.427 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRRX2, PMX2, PRX2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99811
#2: DNA chain
DNA (5'-D(*TP*AP*CP*TP*AP*AP*TP*TP*AP*GP*TP*A)-3')


Mass: 3660.428 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O
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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M Calcium acetate hydrate, 0.18M sodium cacodylate trihydrate pH 6.5, 16% w/v PEG 8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.52→48.45 Å / Num. obs: 126183 / % possible obs: 99.48 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.5
Reflection shellResolution: 1.52→1.57 Å / Rmerge(I) obs: 1.632 / Num. unique obs: 6336

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→48.45 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 4048 3.21 %
Rwork0.1915 --
obs0.1926 126183 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 1470 0 444 3431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073231
X-RAY DIFFRACTIONf_angle_d0.9374653
X-RAY DIFFRACTIONf_dihedral_angle_d28.886923
X-RAY DIFFRACTIONf_chiral_restr0.043498
X-RAY DIFFRACTIONf_plane_restr0.006364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.540.35381400.33894256X-RAY DIFFRACTION100
1.54-1.560.31581430.3114179X-RAY DIFFRACTION100
1.56-1.580.2791250.27824248X-RAY DIFFRACTION99
1.58-1.60.28851360.28314185X-RAY DIFFRACTION100
1.6-1.620.26211400.26684198X-RAY DIFFRACTION99
1.62-1.640.28841340.25444242X-RAY DIFFRACTION98
1.64-1.670.2881400.24694064X-RAY DIFFRACTION98
1.67-1.690.27571330.25664117X-RAY DIFFRACTION97
1.69-1.720.30371360.23794204X-RAY DIFFRACTION99
1.72-1.750.26631300.23774188X-RAY DIFFRACTION100
1.75-1.780.241400.23234319X-RAY DIFFRACTION100
1.78-1.820.29511440.23244114X-RAY DIFFRACTION99
1.82-1.850.26621360.2314269X-RAY DIFFRACTION100
1.85-1.890.23321360.23084267X-RAY DIFFRACTION100
1.89-1.940.28351480.22444226X-RAY DIFFRACTION100
1.94-1.990.2711360.22524217X-RAY DIFFRACTION100
1.99-2.040.22691480.21264206X-RAY DIFFRACTION100
2.04-2.10.25681400.20624234X-RAY DIFFRACTION100
2.1-2.170.19671400.19864226X-RAY DIFFRACTION100
2.17-2.240.23351520.20674210X-RAY DIFFRACTION100
2.25-2.330.23071440.20144288X-RAY DIFFRACTION100
2.34-2.440.24481440.20034272X-RAY DIFFRACTION100
2.44-2.570.25361160.21784202X-RAY DIFFRACTION100
2.57-2.730.2331340.20854224X-RAY DIFFRACTION100
2.73-2.940.19841480.19884267X-RAY DIFFRACTION100
2.94-3.240.2531360.19374202X-RAY DIFFRACTION99
3.24-3.710.19691560.16214110X-RAY DIFFRACTION98
3.71-4.670.22281440.13674207X-RAY DIFFRACTION100
4.67-48.450.16271490.15754194X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.3252 Å / Origin y: -26.3861 Å / Origin z: -2.3695 Å
111213212223313233
T0.1924 Å20.0073 Å20.0007 Å2-0.1704 Å2-0.0037 Å2--0.1485 Å2
L0.2044 °20.0256 °20.0582 °2-0.073 °2-0.0114 °2---0.0578 °2
S0.0209 Å °-0.0322 Å °-0.0126 Å °-0.0087 Å °-0.0069 Å °0.0015 Å °0.0656 Å °0.0051 Å °-0 Å °
Refinement TLS groupSelection details: all

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