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- PDB-9bvd: Crystal structure of SRY HMG box bound to DNA -

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Basic information

Entry
Database: PDB / ID: 9bvd
TitleCrystal structure of SRY HMG box bound to DNA
Components
  • DNA (5'-D(*CP*AP*CP*TP*AP*GP*CP*AP*TP*TP*GP*TP*TP*TP*GP*GP*G)-3')
  • DNA (5'-D(*GP*CP*CP*CP*AP*AP*AP*CP*AP*AP*TP*GP*CP*TP*AP*GP*TP*G)-3')
  • Sex-determining region Y protein
KeywordsDNA BINDING PROTEIN/DNA / DNA-complex / transcription factor / sex-determination / SRY / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of male gonad development / Transcriptional regulation of testis differentiation / sex differentiation / male sex determination / Deactivation of the beta-catenin transactivating complex / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding ...positive regulation of male gonad development / Transcriptional regulation of testis differentiation / sex differentiation / male sex determination / Deactivation of the beta-catenin transactivating complex / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription factor SRY / : / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Sex-determining region Y protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsGeorgiadis, M.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Role of nucleobase-specific interactions in the binding and bending of DNA by human male sex determination factor SRY.
Authors: Racca, J.D. / Chen, Y.S. / Brabender, A.R. / Battistin, U. / Weiss, M.A. / Georgiadis, M.M.
History
DepositionMay 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Sex-determining region Y protein
A: DNA (5'-D(*CP*AP*CP*TP*AP*GP*CP*AP*TP*TP*GP*TP*TP*TP*GP*GP*G)-3')
B: DNA (5'-D(*GP*CP*CP*CP*AP*AP*AP*CP*AP*AP*TP*GP*CP*TP*AP*GP*TP*G)-3')
F: Sex-determining region Y protein
D: DNA (5'-D(*CP*AP*CP*TP*AP*GP*CP*AP*TP*TP*GP*TP*TP*TP*GP*GP*G)-3')
E: DNA (5'-D(*GP*CP*CP*CP*AP*AP*AP*CP*AP*AP*TP*GP*CP*TP*AP*GP*TP*G)-3')
I: Sex-determining region Y protein
G: DNA (5'-D(*CP*AP*CP*TP*AP*GP*CP*AP*TP*TP*GP*TP*TP*TP*GP*GP*G)-3')
H: DNA (5'-D(*GP*CP*CP*CP*AP*AP*AP*CP*AP*AP*TP*GP*CP*TP*AP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,17511
Polymers62,0519
Non-polymers1242
Water28816
1
C: Sex-determining region Y protein
A: DNA (5'-D(*CP*AP*CP*TP*AP*GP*CP*AP*TP*TP*GP*TP*TP*TP*GP*GP*G)-3')
B: DNA (5'-D(*GP*CP*CP*CP*AP*AP*AP*CP*AP*AP*TP*GP*CP*TP*AP*GP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)20,6843
Polymers20,6843
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-17 kcal/mol
Surface area10580 Å2
MethodPISA
2
F: Sex-determining region Y protein
D: DNA (5'-D(*CP*AP*CP*TP*AP*GP*CP*AP*TP*TP*GP*TP*TP*TP*GP*GP*G)-3')
E: DNA (5'-D(*GP*CP*CP*CP*AP*AP*AP*CP*AP*AP*TP*GP*CP*TP*AP*GP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)20,6843
Polymers20,6843
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-12 kcal/mol
Surface area10430 Å2
MethodPISA
3
I: Sex-determining region Y protein
G: DNA (5'-D(*CP*AP*CP*TP*AP*GP*CP*AP*TP*TP*GP*TP*TP*TP*GP*GP*G)-3')
H: DNA (5'-D(*GP*CP*CP*CP*AP*AP*AP*CP*AP*AP*TP*GP*CP*TP*AP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8085
Polymers20,6843
Non-polymers1242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-13 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.506, 91.226, 73.756
Angle α, β, γ (deg.)90.000, 106.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sex-determining region Y protein / Testis-determining factor


Mass: 9940.705 Da / Num. of mol.: 3 / Fragment: HMG box, residues 59-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRY, TDF / Production host: Escherichia coli (E. coli) / References: UniProt: Q05066
#2: DNA chain DNA (5'-D(*CP*AP*CP*TP*AP*GP*CP*AP*TP*TP*GP*TP*TP*TP*GP*GP*G)-3')


Mass: 5233.395 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*CP*CP*AP*AP*AP*CP*AP*AP*TP*GP*CP*TP*AP*GP*TP*G)-3')


Mass: 5509.594 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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.: 16 / 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: 3.1 Å3/Da / Density % sol: 60.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M KCl, 0.1M Mg(OAc)2, 0.05M MES 6.5, 8% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.48→57.09 Å / Num. obs: 26500 / % possible obs: 98.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 68.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.023 / Rrim(I) all: 0.042 / Net I/σ(I): 12 / Num. measured all: 91922
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.48-2.613.50.4161363338880.9460.260.4922.599
7.83-57.093.30.03128788670.9960.020.03824.396.7

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y60

4y60


Resolution: 2.48→35.38 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 1317 4.99 %
Rwork0.1995 25101 -
obs0.2012 26418 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.56 Å2 / Biso mean: 94.1168 Å2 / Biso min: 57.03 Å2
Refinement stepCycle: final / Resolution: 2.48→35.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 2057 8 16 4010
Biso mean--143.35 82.2 -
Num. residues----320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.48-2.580.33791550.32452757291299
2.58-2.690.33131540.30422789294398
2.69-2.830.3451470.31472744289197
2.84-3.010.3871410.31432779292098
3.01-3.250.24841460.22592801294798
3.25-3.570.22751360.20392800293698
3.57-4.090.23911430.19572790293398
4.09-5.150.21051360.17012842297899
5.15-35.380.19531590.16032799295897
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)
12.2083-1.54930.69755.7472-0.60912.3628-0.32220.08040.2874-0.62660.07970.2215-0.2315-0.06370.11280.6031-0.0256-0.03770.66940.05860.752428.4892-4.981559.0291
22.223-0.60741.39841.10210.54312.0005-0.0497-0.504-0.4250.3143-0.08650.0411-0.0579-0.01940.1970.77680.05110.06830.75020.07510.754930.9238-16.924672.4653
35.9352-2.4887-3.38199.5079-5.05946.9213-1.5215-1.3122-0.71571.8211.7191-0.36891.3867-0.6546-0.10671.41980.36340.33621.2423-0.05951.750310.46623.458974.4892
43.43891.3679-0.86611.3071-0.64084.1394-0.0619-0.5389-0.67180.07610.09181.60330.3816-1.3577-0.12780.7209-0.07460.12720.95380.09251.281416.6549-16.147564.9565
51.91480.15841.47225.8978-0.92486.1889-1.13720.6715-1.1449-0.821-0.0842-0.2923-0.24810.76861.5171.2677-0.42550.20411.2040.06451.72513.4153-29.183162.3258
63.0626-1.5025-0.61162.8762-2.12582.61460.25190.030.1654-0.0080.3191.2344-0.4562-1.1045-0.49350.67310.17040.10240.9530.07731.264616.007-2.387766.7734
73.21231.19481.6024.1851-0.71181.97040.06260.18730.4238-0.90320.04291.06310.2232-0.15550.03540.6268-0.0782-0.08610.62270.12650.662833.10278.780783.071
82.3303-0.71240.476.22942.04081.48930.2499-0.0737-0.22440.72230.103-1.92920.29830.2896-0.39320.84770.0638-0.01950.78350.00770.659642.13364.726785.744
97.0412-0.6729-1.15714.03790.02465.58150.2824-0.56770.7122-0.88160.09760.7927-0.4872-0.3345-0.06720.72010.0074-0.02810.63420.02461.019830.201322.515382.4586
105.2349-2.982.7466.4005-2.11942.0587-0.41940.72670.12540.13830.32431.15180.305-1.42110.26430.75230.06060.25021.3020.05831.34419.933120.264298.2483
113.14690.57730.01096.3646-2.15365.35840.0959-0.32061.5173-1.50990.64952.3534-0.0184-0.4384-0.79121.4771-0.40040.23951.20780.36321.359621.108-7.574998.4808
128.17294.044-0.7762.5675-2.19885.63621.7038-2.96660.3032.1944-1.86881.43461.898-0.3580.02381.3986-0.3206-0.04920.9048-0.03090.850235.61944.912995.7641
132.9103-0.341-0.94472.2870.96044.00630.5155-0.39860.54171.26430.29210.4345-0.5237-0.4494-0.68631.0884-0.02820.33610.883-0.12610.902731.610421.855102.6721
140.7888-1.4767-1.57735.78680.43994.15510.1443-0.26950.13170.75910.8027-0.9093-0.4899-0.2074-0.74741.03450.06830.22360.8605-0.12831.009633.717118.4774101.7165
151.8687-0.7355-2.27133.6671-2.53157.27230.1421-0.7116-0.4595-0.03130.1010.63991.37171.5553-0.25061.2319-0.25850.06711.17160.32020.841829.5342-4.519795.1601
164.5122-1.47420.95585.9022-1.03933.12980.6376-0.032-0.766-1.1250.3062-0.42540.71550.0908-0.74430.6909-0.1119-0.06030.6231-0.15480.563351.836-18.901884.4801
176.65080.8261-0.0617.7359-5.91584.59020.0508-0.75540.69250.5415-0.20460.3053-2.6747-0.2381-0.16810.9382-0.01130.07330.7564-0.09740.80945.1366-4.344583.5596
181.41151.2435-0.83335.75760.43813.4068-0.2677-0.0455-0.21820.10540.3472-0.62130.16850.1113-0.00160.6162-0.0183-0.0760.666-0.06810.662950.024-26.269186.7959
193.1259-1.5798-0.79663.3493-0.62140.65320.11360.2422-0.08710.4485-0.1494-1.5795-0.0904-0.0995-0.170.8944-0.1558-0.31181.6462-0.13531.403366.7836-25.9014100.0398
203.4263.35270.41846.05520.30624.24860.5675-1.59270.96841.571-0.5795-1.7342-0.68130.7608-0.19471.0773-0.1441-0.20.932-0.26581.345354.802-9.749596.5324
210.55030.054-0.34182.62630.25370.2270.6611-1.8762-1.15761.1530.9567-1.32950.1-0.08810.13411.43040.2176-0.65241.52860.07310.89856.044-29.5391107.9748
221.2707-2.46970.83755.6601-0.70422.0184-0.0834-0.8443-0.62931.47511.00030.6574-0.01030.0471-0.65851.43330.1496-0.40310.89190.15331.251552.282-25.5683104.5529
232.63920.14341.92585.30240.62794.66970.2215-1.37030.97291.5515-0.9828-0.0396-1.2109-1.45770.51391.213-0.3019-0.00961.1879-0.62621.633355.1345-2.747193.8873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 4 through 47 )C4 - 47
2X-RAY DIFFRACTION2chain 'C' and (resid 48 through 77 )C48 - 77
3X-RAY DIFFRACTION3chain 'A' and (resid 0 through 4 )A0 - 4
4X-RAY DIFFRACTION4chain 'A' and (resid 5 through 16 )A5 - 16
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 4 )B0 - 4
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 16 )B5 - 16
7X-RAY DIFFRACTION7chain 'F' and (resid 5 through 27 )F5 - 27
8X-RAY DIFFRACTION8chain 'F' and (resid 28 through 47 )F28 - 47
9X-RAY DIFFRACTION9chain 'F' and (resid 48 through 68 )F48 - 68
10X-RAY DIFFRACTION10chain 'F' and (resid 69 through 77 )F69 - 77
11X-RAY DIFFRACTION11chain 'D' and (resid 0 through 4 )D0 - 4
12X-RAY DIFFRACTION12chain 'D' and (resid 5 through 9 )D5 - 9
13X-RAY DIFFRACTION13chain 'D' and (resid 10 through 16 )D10 - 16
14X-RAY DIFFRACTION14chain 'E' and (resid 0 through 9 )E0 - 9
15X-RAY DIFFRACTION15chain 'E' and (resid 10 through 16 )E10 - 16
16X-RAY DIFFRACTION16chain 'I' and (resid 6 through 26 )I6 - 26
17X-RAY DIFFRACTION17chain 'I' and (resid 27 through 31 )I27 - 31
18X-RAY DIFFRACTION18chain 'I' and (resid 32 through 67 )I32 - 67
19X-RAY DIFFRACTION19chain 'I' and (resid 68 through 77 )I68 - 77
20X-RAY DIFFRACTION20chain 'G' and (resid 1 through 10 )G1 - 10
21X-RAY DIFFRACTION21chain 'G' and (resid 11 through 16 )G11 - 16
22X-RAY DIFFRACTION22chain 'H' and (resid 0 through 9 )H0 - 9
23X-RAY DIFFRACTION23chain 'H' and (resid 10 through 16 )H10 - 16

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