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- PDB-4ndy: Human MHF1-MHF2 DNA complex -

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Basic information

Entry
Database: PDB / ID: 4ndy
TitleHuman MHF1-MHF2 DNA complex
Components
  • (DNA (26-MER)) x 2
  • Centromere protein S
  • Centromere protein X
KeywordsDNA Binding Protein/DNA / Histone Fold / DNA repair / genome maintenance / centromere construction / Fanconi Anemia / FancM / nucleus / DNA Binding Protein-DNA complex
Function / homology
Function and homology information


FANCM-MHF complex / Fanconi anaemia nuclear complex / inner kinetochore / resolution of meiotic recombination intermediates / kinetochore assembly / replication fork processing / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / interstrand cross-link repair / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation ...FANCM-MHF complex / Fanconi anaemia nuclear complex / inner kinetochore / resolution of meiotic recombination intermediates / kinetochore assembly / replication fork processing / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / interstrand cross-link repair / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / positive regulation of protein ubiquitination / chromosome segregation / RHO GTPases Activate Formins / Fanconi Anemia Pathway / PKR-mediated signaling / Separation of Sister Chromatids / protein heterodimerization activity / cell division / DNA repair / DNA damage response / chromatin binding / chromatin / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / Centromere protein X / Centromere protein S
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic DNA (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.999 Å
AuthorsZhao, Q. / Saro, D. / Sachpatzidis, A. / Sung, P. / Xiong, Y.
CitationJournal: Nat Commun / Year: 2014
Title: The MHF complex senses branched DNA by binding a pair of crossover DNA duplexes.
Authors: Zhao, Q. / Saro, D. / Sachpatzidis, A. / Singh, T.R. / Schlingman, D. / Zheng, X.F. / Mack, A. / Tsai, M.S. / Mochrie, S. / Regan, L. / Meetei, A.R. / Sung, P. / Xiong, Y.
History
DepositionOct 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA (26-MER)
F: DNA (26-MER)
O: DNA (26-MER)
P: DNA (26-MER)
C: Centromere protein S
D: Centromere protein X
G: Centromere protein S
H: Centromere protein X
A: Centromere protein S
B: Centromere protein X
I: Centromere protein S
J: Centromere protein S
K: Centromere protein S
L: Centromere protein X
M: Centromere protein X
N: Centromere protein X
Q: Centromere protein S
R: Centromere protein S
S: Centromere protein S
T: Centromere protein S
U: Centromere protein X
V: Centromere protein X
W: Centromere protein X
X: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)236,83224
Polymers236,83224
Non-polymers00
Water0
1
E: DNA (26-MER)
F: DNA (26-MER)
I: Centromere protein S
J: Centromere protein S
M: Centromere protein X
N: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)56,9446
Polymers56,9446
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (26-MER)
F: DNA (26-MER)
O: DNA (26-MER)
P: DNA (26-MER)
K: Centromere protein S
L: Centromere protein X
T: Centromere protein S
U: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)72,9068
Polymers72,9068
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
O: DNA (26-MER)
P: DNA (26-MER)
Q: Centromere protein S
R: Centromere protein S
V: Centromere protein X
W: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)56,9446
Polymers56,9446
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Centromere protein S
B: Centromere protein X
S: Centromere protein S
X: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)40,9814
Polymers40,9814
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: Centromere protein S
D: Centromere protein X
G: Centromere protein S
H: Centromere protein X


Theoretical massNumber of molelcules
Total (without water)40,9814
Polymers40,9814
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)250.098, 250.098, 65.561
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3

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Components

#1: DNA chain DNA (26-MER)


Mass: 8098.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic DNA (others)
#2: DNA chain DNA (26-MER)


Mass: 7864.056 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic DNA (others)
#3: Protein
Centromere protein S / / CENP-S / Apoptosis-inducing TAF9-like domain-containing protein 1 / FANCM-interacting histone fold ...CENP-S / Apoptosis-inducing TAF9-like domain-containing protein 1 / FANCM-interacting histone fold protein 1 / Fanconi anemia-associated polypeptide of 16 kDa


Mass: 12091.949 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APITD1, CENPS, FAAP16, MHF1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rossetta 2 / References: UniProt: Q8N2Z9
#4: Protein
Centromere protein X / / CENP-X / FANCM-interacting histone fold protein 2 / Fanconi anemia-associated polypeptide of 10 kDa ...CENP-X / FANCM-interacting histone fold protein 2 / Fanconi anemia-associated polypeptide of 10 kDa / Retinoic acid-inducible gene D9 protein homolog / Stimulated by retinoic acid gene 13 protein homolog


Mass: 8398.796 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STRA13, CENPX, FAAP10, MHF2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rossetta 2 / References: UniProt: A8MT69

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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: 5 Å3/Da / Density % sol: 75.39 %
Crystal growTemperature: 300 K / Method: micro-batch under oil
Details: 0.1-0.3M Ammonium Phosphate, Micro-batch under oil, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.461
11-K, -H, -L20.046
11-h,-k,l30.045
11K, H, -L40.449
ReflectionResolution: 6.99→108.3 Å / Num. all: 7215 / Num. obs: 7171 / % possible obs: 99.39 % / Observed criterion σ(F): 0
Reflection shellResolution: 6.99→100 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.11data extraction
APEXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.7.0029refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.999→108.3 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.848 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 613.494 / SU ML: 2.308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.648 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2791 439 6.1 %RANDOM
Rwork0.2419 ---
obs0.244 7171 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso max: 616.81 Å2 / Biso mean: 310.2741 Å2 / Biso min: 158 Å2
Baniso -1Baniso -2Baniso -3
1--20.27 Å20 Å20 Å2
2---20.27 Å20 Å2
3---40.53 Å2
Refinement stepCycle: LAST / Resolution: 6.999→108.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13734 2132 0 0 15866
LS refinement shellResolution: 6.999→7.178 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 75 -
Rwork0.265 436 -
all-511 -
obs--94.98 %
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)
14.8151-2.3805-2.2122.0470.99892.307-1.75411.01241.3531.37980.8261-0.75241.2365-0.47020.9282.150.09870.03332.3090.08062.5105114.750528.249846.1394
215.3798-6-4.70214.1412.38593.8032-3.01751.80931.45851.49931.2909-0.62451.4702-0.19051.72652.5561-0.4293-0.11322.2623-0.05292.1311115.339427.213544.6338
31.87490.42010.45840.81450.39331.3162-1.2183-1.6108-0.8368-1.33850.3567-0.6402-1.3959-0.57090.86162.86030.11240.2472.58350.08112.5563113.8809-29.321216.64
430.649115.50599.407210.33685.8213.7425-0.3268-0.41230.8081-0.3515-0.20180.5117-0.76-0.25610.52863.82770.37650.47122.9352-0.13882.454114.0304-28.408317.5782
53.56871.1023-3.60419.5115-5.95636.31661.1998-0.038-0.0421-0.0241-1.1861.0776-1.16711.2802-0.01383.0881-0.1712-1.06324.08210.02862.482530.0341-34.0163-11.2021
60.19370.1982-0.35041.07770.80222.9957-0.12720.0326-0.31390.7983-0.8019-0.0840.71050.72950.92913.8726-0.2327-1.09423.6474-0.2454.377731.307-38.8681-11.8733
72.89734.96250.171713.3923-1.83641.02180.33010.22520.08231.7694-1.2499-0.679-0.94770.52050.91982.70680.17870.2572.8345-0.33963.54436.231-53.2284-6.9962
811.4608-9.9289-6.886215.669711.61668.69450.3740.3316-0.8840.6399-1.090.47320.4587-1.00820.7162.1070.06070.18851.99570.21022.84949.4537-56.42-6.6125
92.01290.0446-3.18854.3864.499410.05430.2370.4174-0.09880.568-0.160.17810.3092-0.4973-0.07711.5853-0.19220.2531.51270.10961.611939.9908-94.8477-5.7006
101.27580.1417-2.26256.48124.3939.8067-0.2092-1.48151.0418-1.66380.0330.22280.5713.410.17622.0594-0.0806-0.01132.39-0.03893.247439.0903-90.7021-5.1509
1112.4546-0.0466-3.332310.41610.27040.9945-0.7218-1.6084-0.3578-0.56640.5128-1.40710.62660.46450.20892.00950.3731-0.13592.21540.01161.125580.955450.076441.5295
125.28195.63871.2136.0221.28440.36630.6114-0.19240.16110.6549-0.30680.20590.11910.2801-0.30462.42830.2363-0.10772.0023-0.12522.369768.635945.116413.7696
130.436-0.62180.60484.80922.28983.8849-0.804-0.17660.2667-0.20230.5396-0.2993-1.3009-0.37990.26442.51460.0063-0.2942.62480.00682.1977100.555116.259830.8073
140.9262-1.84680.06114.8141-0.91040.5985-0.5960.1902-0.92710.0110.3881.12560.1934-0.82690.2082.7241-0.2515-0.39843.2831-0.54333.283794.059312.784930.9018
1515.2162-5.18482.097113.65511.1064.08880.40770.1274-0.4455-0.2812-0.48680.3158-1.11510.21370.07912.271-0.43790.15222.43950.06470.045773.642852.364540.4145
160.1757-0.65790.37773.9338-1.76281.0572-0.3267-0.35210.1660.317-0.0594-0.27410.2539-0.55540.38622.17650.0510.11361.9735-0.20432.131664.675747.825914.0699
1720.06465.62942.37255.1594-1.99042.4836-0.8425-1.0301-1.1141-0.0440.0869-1.0967-0.7663-0.21850.75552.2540.17310.02161.8392-0.15271.189480.2185-51.358720.187
188.07210.6657-2.04247.9288-8.12238.77951.4234-0.3469-1.06740.1655-0.35511.01120.2610.5218-1.06842.3448-0.0925-0.52361.6691-0.10822.177469.9504-45.663346.0937
1910.4724-9.313812.26769.2801-9.265917.371-0.03920.2926-0.16730.61440.19840.37910.86820.3713-0.15930.9288-0.430.6042.08850.38931.945461.7408-82.05211.6818
207.83222.7284-2.1691.34650.857513.2518-0.51343.1023-0.35860.24980.39370.41770.7219-0.36590.11972.6379-0.37040.56244.26740.15243.0502101.4448-16.618229.8638
213.85765.0552-0.02667.1249-0.30460.2191-1.08720.87061.07090.00131.35490.29530.05-0.9238-0.26774.122-0.4065-0.10034.4901-0.3794.592394.8687-12.492129.394
228.16621.5432-0.2186.0477-4.98044.4381-0.63021.3562-0.11060.80771.13020.1773-0.216-0.5451-0.53.20520.14730.27512.0256-0.32981.689373.1514-53.214921.1782
230.86661.00190.05494.44815.527910.4896-0.553-0.2240.5443-0.1512-0.2390.9116-0.3015-0.92980.79211.92030.0881-0.11572.0540.12412.086366.6386-47.425844.8748
243.87122.04931.89433.5904-0.0173.9237-0.71181.09750.53220.7959-0.6778-0.5131-0.66331.70111.38961.7395-0.14490.25562.07510.1222.598758.9597-78.77371.3104
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E1 - 26
2X-RAY DIFFRACTION2F1 - 26
3X-RAY DIFFRACTION3O1 - 26
4X-RAY DIFFRACTION4P1 - 26
5X-RAY DIFFRACTION5C14 - 106
6X-RAY DIFFRACTION6D8 - 81
7X-RAY DIFFRACTION7G14 - 106
8X-RAY DIFFRACTION8H8 - 81
9X-RAY DIFFRACTION9A14 - 106
10X-RAY DIFFRACTION10B8 - 81
11X-RAY DIFFRACTION11I14 - 118
12X-RAY DIFFRACTION12J14 - 106
13X-RAY DIFFRACTION13K14 - 118
14X-RAY DIFFRACTION14L8 - 81
15X-RAY DIFFRACTION15M8 - 81
16X-RAY DIFFRACTION16N8 - 81
17X-RAY DIFFRACTION17Q14 - 118
18X-RAY DIFFRACTION18R14 - 106
19X-RAY DIFFRACTION19S14 - 106
20X-RAY DIFFRACTION20T14 - 118
21X-RAY DIFFRACTION21U8 - 81
22X-RAY DIFFRACTION22V8 - 81
23X-RAY DIFFRACTION23W8 - 81
24X-RAY DIFFRACTION24X8 - 81

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