[English] 日本語
Yorodumi
- PDB-9bvd: Crystal structure of SRY HMG box bound to DNA -

+
Open data


ID or keywords:

Loading...

-
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 / brain development / neuron differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / 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 / brain development / neuron differentiation / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more