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- PDB-6n64: Crystal structure of mouse SMCHD1 hinge domain -

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Basic information

Entry
Database: PDB / ID: 6n64
TitleCrystal structure of mouse SMCHD1 hinge domain
Components
  • Structural maintenance of chromosomes flexible hinge domain-containing protein 1
  • Uncharacterized peptide from Structural maintenance of chromosomes flexible hinge domain-containing protein 1
KeywordsDNA BINDING PROTEIN / SMCHD1 Epigenetic control DNA binding SMC protein
Function / homology
Function and homology information


: / : / : / nose development / chromosome, telomeric region => GO:0000781 / Barr body / dosage compensation by inactivation of X chromosome / positive regulation of double-strand break repair via nonhomologous end joining / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / negative regulation of double-strand break repair via homologous recombination ...: / : / : / nose development / chromosome, telomeric region => GO:0000781 / Barr body / dosage compensation by inactivation of X chromosome / positive regulation of double-strand break repair via nonhomologous end joining / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / negative regulation of double-strand break repair via homologous recombination / positive regulation of DNA repair / double-strand break repair / site of double-strand break / protein homodimerization activity / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
Structural maintenance of chromosomes flexible hinge domain-containing protein 1 / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Structural maintenance of chromosomes flexible hinge domain-containing protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsBirkinshaw, R.W. / Chen, K. / Czabotar, P.E. / Blewitt, M.E. / Murphy, J.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1098290 Australia
CitationJournal: Sci.Signal. / Year: 2020
Title: Crystal structure of the hinge domain of Smchd1 reveals its dimerization mode and nucleic acid-binding residues.
Authors: Chen, K. / Birkinshaw, R.W. / Gurzau, A.D. / Wanigasuriya, I. / Wang, R. / Iminitoff, M. / Sandow, J.J. / Young, S.N. / Hennessy, P.J. / Willson, T.A. / Heckmann, D.A. / Webb, A.I. / ...Authors: Chen, K. / Birkinshaw, R.W. / Gurzau, A.D. / Wanigasuriya, I. / Wang, R. / Iminitoff, M. / Sandow, J.J. / Young, S.N. / Hennessy, P.J. / Willson, T.A. / Heckmann, D.A. / Webb, A.I. / Blewitt, M.E. / Czabotar, P.E. / Murphy, J.M.
History
DepositionNov 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
B: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
C: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
D: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
E: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
F: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
G: Uncharacterized peptide from Structural maintenance of chromosomes flexible hinge domain-containing protein 1
H: Uncharacterized peptide from Structural maintenance of chromosomes flexible hinge domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)155,9408
Polymers155,9408
Non-polymers00
Water0
1
A: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
B: Structural maintenance of chromosomes flexible hinge domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)50,7772
Polymers50,7772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-11 kcal/mol
Surface area17270 Å2
MethodPISA
2
C: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
D: Structural maintenance of chromosomes flexible hinge domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)50,7772
Polymers50,7772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-13 kcal/mol
Surface area17010 Å2
MethodPISA
3
E: Structural maintenance of chromosomes flexible hinge domain-containing protein 1
F: Structural maintenance of chromosomes flexible hinge domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)50,7772
Polymers50,7772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-12 kcal/mol
Surface area17140 Å2
MethodPISA
4
G: Uncharacterized peptide from Structural maintenance of chromosomes flexible hinge domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)1,8051
Polymers1,8051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1000 Å2
MethodPISA
5
H: Uncharacterized peptide from Structural maintenance of chromosomes flexible hinge domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)1,8051
Polymers1,8051
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.549, 123.549, 232.869
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Structural maintenance of chromosomes flexible hinge domain-containing protein 1 / SMC hinge domain-containing protein 1


Mass: 25388.342 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smchd1, Kiaa0650 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6P5D8, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Protein/peptide Uncharacterized peptide from Structural maintenance of chromosomes flexible hinge domain-containing protein 1


Mass: 1805.216 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Smchd1, Kiaa0650 / Production host: Escherichia coli (E. coli)
References: Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
Has ligand of interestN
Sequence detailsChains G and H are portions of helix that are included in the SMCHD1 construct, but could not be ...Chains G and H are portions of helix that are included in the SMCHD1 construct, but could not be assigned to one of the chains A-F. In addition the resolution was not sufficient to dock sequence so they have been modeled as poly alanine helices, and since the registry is unknown, they are marked as UNKs. There should be 6 copies of these, but only 2 were sufficiently ordered to model as helices.

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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: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal growTemperature: 281 K / Method: vapor diffusion / pH: 9.35
Details: 0.1 M Sodium Bicine pH 9.35, 0.18 M MgCl2, 20% (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2014
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.3→48.45 Å / Num. obs: 27936 / % possible obs: 99.87 % / Redundancy: 17.7 % / Biso Wilson estimate: 117.12 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.04826 / Rrim(I) all: 0.2053 / Net I/σ(I): 14.81
Reflection shellResolution: 3.3→3.418 Å / Redundancy: 17.9 % / Mean I/σ(I) obs: 2.03 / Num. unique obs: 2722 / CC1/2: 0.674 / Rpim(I) all: 0.461 / Rrim(I) all: 1.956 / % possible all: 99.71

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→48.45 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.424
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1399 5.01 %RANDOM
Rwork0.204 ---
obs0.206 27936 99.9 %-
Displacement parametersBiso max: 220.68 Å2 / Biso mean: 117.23 Å2 / Biso min: 61.09 Å2
Baniso -1Baniso -2Baniso -3
1-4.0151 Å20 Å20 Å2
2--4.0151 Å20 Å2
3----8.0303 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: final / Resolution: 3.3→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8412 0 0 0 8412
Num. residues----1071
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2978SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1460HARMONIC5
X-RAY DIFFRACTIONt_it8602HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1146SEMIHARMONIC5
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_contact9922SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8602HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11672HARMONIC21.16
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion21.02
LS refinement shellResolution: 3.3→3.32 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3534 25 4.47 %
Rwork0.2636 534 -
all0.2675 559 -
obs--94.52 %
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)
11.99591.99250.76973.9023.45414.5798-0.42980.24930.3993-0.67250.40890.0477-0.76110.07870.0210.1238-0.14360.0244-0.27510.02-0.140140.703848.916563.3233
24.20982.4212-0.89144.01071.67733.0835-0.13020.1046-0.70770.28990.6407-1.08850.30040.7215-0.5105-0.15030.0762-0.0025-0.2687-0.25770.041154.473335.248471.9755
32.6598-0.1697-0.54424.4625-1.93334.0525-0.1302-0.07480.00250.73190.3862-0.2651-0.5471-0.0466-0.2560.01840.0957-0.0902-0.2025-0.0448-0.180887.855767.8883103.073
42.5807-0.99540.93564.092-1.95013.59560.00980.1498-0.3724-0.46350.3211-0.07830.821-0.1915-0.33090.001-0.1282-0.0471-0.2125-0.0872-0.114987.276353.451787.0686
56.4143-3.69450.4113.866-0.33611.4381-0.18160.04990.7869-0.27170.1637-0.7939-0.1796-0.10190.0179-0.1305-0.06260.0107-0.3088-0.1380.083753.517290.200389.4575
64.3003-2.8488-0.66836.01382.19442.4376-0.6304-0.4346-0.60510.39620.45810.30870.4713-0.44330.1723-0.03530.00260.0429-0.20920.0733-0.174938.93876.340496.6238
70-0.12450.228700.29160-0.0006-0.0147-0.0034-0.01260.01050.0167-0.0043-0.0039-0.00990.09240.11270.027-0.050.0507-0.000857.974617.941987.8769
800.7754-0.87350-0.076800.020.0430.0918-0.0803-0.0089-0.0408-0.01910.0041-0.0112-0.1194-0.15840.2177-0.01010.11030.194984.7598.4744114.113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1715 - 1884
2X-RAY DIFFRACTION2{ B|* }B1712 - 1884
3X-RAY DIFFRACTION3{ C|* }C1710 - 1884
4X-RAY DIFFRACTION4{ D|* }D1710 - 1884
5X-RAY DIFFRACTION5{ E|* }E1714 - 1886
6X-RAY DIFFRACTION6{ F|* }F1713 - 1884
7X-RAY DIFFRACTION7{ G|* }G273 - 284
8X-RAY DIFFRACTION8{ H|* }H273 - 293

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