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- PDB-9d9r: X-ray structure of ALX4 homeodomain dimer bound to DNA -

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Basic information

Entry
Database: PDB / ID: 9d9r
TitleX-ray structure of ALX4 homeodomain dimer bound to DNA
Components
  • DNA (5'-D(*CP*GP*CP*TP*AP*AP*TP*TP*CP*AP*AP*TP*TP*AP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*TP*AP*AP*TP*TP*GP*AP*AP*TP*TP*AP*GP*CP*G)-3')
  • Homeobox protein aristaless-like 4
KeywordsTRANSCRIPTION/DNA / ALX4 / paired-like homeodomain / transcription factor / TRANSCRIPTION / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


HMG box domain binding / embryonic skeletal system morphogenesis / digestive tract development / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / anterior/posterior pattern specification / embryonic digit morphogenesis / muscle organ development / roof of mouth development / hair follicle development ...HMG box domain binding / embryonic skeletal system morphogenesis / digestive tract development / embryonic forelimb morphogenesis / embryonic hindlimb morphogenesis / anterior/posterior pattern specification / embryonic digit morphogenesis / muscle organ development / roof of mouth development / hair follicle development / post-embryonic development / skeletal system development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / chromatin / DNA binding / nucleoplasm / nucleus
Similarity search - Function
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) / Homeobox protein aristaless-like 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.389 Å
AuthorsYuan, Z. / Kovall, R.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)1R03TR004875 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM079428 United States
CitationJournal: To Be Published
Title: Structural and biochemical characterization of the ALX4 dimer reveals novel insights into how disease alleles impact ALX4 function
Authors: Yuan, Z. / Kovall, R.A.
History
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homeobox protein aristaless-like 4
B: Homeobox protein aristaless-like 4
C: DNA (5'-D(*CP*GP*CP*TP*AP*AP*TP*TP*CP*AP*AP*TP*TP*AP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*TP*AP*AP*TP*TP*GP*AP*AP*TP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9166
Polymers29,7924
Non-polymers1242
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, EMSA was used to confirm assembly.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-21 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.460, 70.460, 159.141
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Homeobox protein aristaless-like 4


Mass: 9689.976 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALX4, KIAA1788 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H161
#2: DNA chain DNA (5'-D(*CP*GP*CP*TP*AP*AP*TP*TP*CP*AP*AP*TP*TP*AP*AP*CP*G)-3')


Mass: 5170.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*GP*TP*TP*AP*AP*TP*TP*GP*AP*AP*TP*TP*AP*GP*CP*G)-3')


Mass: 5241.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 3.83 Å3/Da / Density % sol: 67.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.1M Tris pH 7.5, 0.2M Trimethylamine N-oxide, 20% PEG MME 2000

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.389→79.57 Å / Num. obs: 18846 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.987 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.05 / Rrim(I) all: 0.158 / Χ2: 1.01 / Net I/σ(I): 4.7
Reflection shellResolution: 2.39→2.48 Å / % possible obs: 100 % / Redundancy: 9.7 % / Rmerge(I) obs: 3.46 / Num. measured all: 18662 / Num. unique obs: 1933 / CC1/2: 0.638 / Rpim(I) all: 1.169 / Rrim(I) all: 3.657 / Χ2: 1.1 / Net I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (23-JAN-2024)refinement
pointlessdata scaling
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.389→32.21 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.878 / SU R Cruickshank DPI: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.21 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.179
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 961 5.11 %RANDOM
Rwork0.2136 ---
obs0.2149 18810 99.9 %-
Displacement parametersBiso mean: 122.78 Å2
Baniso -1Baniso -2Baniso -3
1--22.8525 Å20 Å20 Å2
2---22.8525 Å20 Å2
3---45.705 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.389→32.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1180 691 8 2 1881
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081989HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.822819HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d617SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes238HARMONIC5
X-RAY DIFFRACTIONt_it1215HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion21.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion247SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1143SEMIHARMONIC4
LS refinement shellResolution: 2.39→2.41 Å / Total num. of bins used: 49
RfactorNum. reflection% reflection
Rfree0.4973 -2.81 %
Rwork0.3774 381 -
all0.3805 392 -
obs--98.72 %
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)
118.481-6.955-0.469315.828-0.09594.9907-0.5454-1.4787-0.63211.25880.12641.43521.3844-0.42840.41910.247-0.24760.0602-0.01310.1186-0.478-39.238719.634631.9155
27.2409-9.63126.820911.6408-5.99345.1217-0.584-0.9793-2.07740.6190.79380.33261.74550.2422-0.20970.87950.40260.1367-0.38550.12070.1146-24.52736.799226.0813
37.8616-0.1705-2.311816.1474-1.925310.5486-0.3890.4496-1.613-0.54540.2104-0.47171.47250.7150.17860.51010.08830.0586-0.2281-0.1257-0.019-26.188210.677716.3761
45.0533-3.0891-0.9747-4.17871.17656.12980.0915-0.954-0.44120.1951-0.004-0.43941.07680.5582-0.08750.25540.13520.0114-0.04340.0615-0.1404-26.562518.220122.3496
517.85029.8117-3.34315.37957.567416.6309-0.54120.5230.1124-0.24591.96790.8931-0.13871.6292-1.4267-0.08680.1733-0.14740.2604-0.1582-0.306-13.186926.494523.7175
623.11036.44710.03528.1144-3.615912.12460.4321.4041-1.8056-1.0635-0.54090.12320.1979-0.76590.10890.0016-0.1335-0.1784-0.0469-0.3252-0.442-42.414319.3927.0069
713.07762.53770.164112.96927.77925.57630.1446-0.2101-0.79370.7128-0.51320.65440.2057-1.55010.3686-0.1099-0.19710.03920.1124-0.0604-0.1817-51.577524.82921.1698
811.2654-8.122-8.720216.57695.047300.2633-0.0029-1.3480.2879-0.55741.10671.892-0.7930.29410.1673-0.3391-0.06260.0838-0.09760.1679-48.863415.843217.1584
96.7228-11.0828-8.011518.22351.04559.99540.70030.17-0.8981.0382-0.47260.5292-1.21590.836-0.2276-0.37580.032-0.17070.4187-0.00960.0619-44.238729.740216.041
1025.8968-8.1825-3.917415.1812-9.33235.0554-0.1409-0.06151.8943-0.76470.7351-0.0155-0.86950.5343-0.59420.3809-0.1681-0.06170.67280.35290.8286-46.833345.905613.5166
1116.9369-0.1767-6.499316.3249-0.391722.65110.8941-0.9933-0.38331.0082-0.1687-1.9009-1.28771.1419-0.72550.24330.0278-0.11990.60520.2066-0.491-25.263421.444738.8985
125.111-7.7333-0.160722.6285-6.75311.3962-0.0578-0.6186-0.17020.5639-0.09820.24520.31210.0940.15610.3012-0.0348-0.0656-0.04960.0392-0.3176-35.108223.294827.3659
1322.988-2.6852-11.52119.36722.492624.94630.73840.44311.6892-1.73390.22680.1180.3961-0.4929-0.9653-0.0023-0.11470.00450.130.0828-0.3287-33.322334.423115.4038
1419.0933-1.8435.04898.0615-2.75772.5812-0.1056-0.0142-1.0677-1.66010.2525-0.64960.3233-0.3418-0.1470.2504-0.1514-0.03510.5029-0.177-0.4796-34.963924.44021.1433
1521.0935-2.5765-9.036412.1683-1.810918.3206-0.33911.30991.5434-0.80350.69890.5922-1.83920.2676-0.35980.45370.0925-0.18150.3361-0.0866-0.4976-39.427730.8918-1.0294
1620.84248.24967.4488.68074.562223.2736-0.81070.6016-0.6126-0.50560.0671-0.02-0.8892-0.16970.74370.0889-0.1932-0.09320.17250.006-0.4031-34.438624.932311.7791
1718.6057-1.7674-11.567712.52562.573416.79310.3777-0.49770.99081.21290.5008-0.4730.53030.7405-0.87850.0545-0.0507-0.10710.12830.0219-0.3153-29.644430.613626.5229
1821.0067-6.20486.88618.0076-6.106310.19120.6793-0.5946-1.07991.7004-0.67081.13981.88380.0027-0.00860.5788-0.084-0.05440.26770.1432-0.4374-33.480219.044539.5087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|210 - 221}
2X-RAY DIFFRACTION2{A|222 - 230}
3X-RAY DIFFRACTION3{A|231 - 254}
4X-RAY DIFFRACTION4{A|255 - 269}
5X-RAY DIFFRACTION5{A|270 - 277}
6X-RAY DIFFRACTION6{B|213 - 226}
7X-RAY DIFFRACTION7{B|227 - 246}
8X-RAY DIFFRACTION8{B|247 - 256}
9X-RAY DIFFRACTION9{B|257 - 271}
10X-RAY DIFFRACTION10{B|272 - 278}
11X-RAY DIFFRACTION11{C|1 - 4}
12X-RAY DIFFRACTION12{C|5 - 8}
13X-RAY DIFFRACTION13{C|9 - 12}
14X-RAY DIFFRACTION14{C|13 - 17}
15X-RAY DIFFRACTION15{D|18 - 21}
16X-RAY DIFFRACTION16{D|22 - 25}
17X-RAY DIFFRACTION17{D|26 - 30}
18X-RAY DIFFRACTION18{D|31 - 34}

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