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- PDB-9ho4: Crystal Structure of the Human Frataxin protein in complex with a... -

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Basic information

Entry
Database: PDB / ID: 9ho4
TitleCrystal Structure of the Human Frataxin protein in complex with a tailored Camelid Nanobody 6B1
Components
  • Camelid Nanobody 6B1
  • Frataxin mature form
KeywordsOXIDOREDUCTASE / Complex / Nanobody / Mitochondrial Regulation / Friedreich Ataxia
Function / homology
Function and homology information


positive regulation of lyase activity / proprioception / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / Complex III assembly / iron chaperone activity / Maturation of TCA enzymes and regulation of TCA cycle / negative regulation of organ growth / mitochondrial respiratory chain complex III assembly / embryo development ending in birth or egg hatching ...positive regulation of lyase activity / proprioception / [4Fe-4S] cluster assembly / Mitochondrial iron-sulfur cluster biogenesis / Complex III assembly / iron chaperone activity / Maturation of TCA enzymes and regulation of TCA cycle / negative regulation of organ growth / mitochondrial respiratory chain complex III assembly / embryo development ending in birth or egg hatching / Mitochondrial protein import / iron-sulfur cluster assembly complex / mitochondrial [2Fe-2S] assembly complex / response to iron ion / oxidative phosphorylation / adult walking behavior / heme biosynthetic process / [2Fe-2S] cluster assembly / negative regulation of multicellular organism growth / organ growth / iron-sulfur cluster assembly / muscle cell cellular homeostasis / negative regulation of release of cytochrome c from mitochondria / ferroxidase / protein autoprocessing / ferroxidase activity / ferric iron binding / protein maturation / iron ion transport / enzyme activator activity / ferrous iron binding / 2 iron, 2 sulfur cluster binding / cellular response to hydrogen peroxide / intracellular iron ion homeostasis / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / cytosol
Similarity search - Function
Frataxin / Frataxin/CyaY / Frataxin conserved site / Frataxin-like domain / Frataxin family signature. / Frataxin family profile. / Frataxin-like domain / Frataxin/CyaY superfamily
Similarity search - Domain/homology
Frataxin, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsGaray-Alvarez, A. / Molina, R. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2020-115331GB-I00 Spain
CitationJournal: To Be Published
Title: Frataxin Stability and Function Modulation by Nanobody Interaction
Authors: Pignataro, M.F. / Frenandez, N.B. / Pavan, M.F. / Garay-Alvarez, A. / Molina, R. / Grossi, J. / Noguera, M. / Vila, A. / Garcia, A. / Gentili, H. / Rodriguez, N.A. / Aran, M. / Hermoso, J.A. ...Authors: Pignataro, M.F. / Frenandez, N.B. / Pavan, M.F. / Garay-Alvarez, A. / Molina, R. / Grossi, J. / Noguera, M. / Vila, A. / Garcia, A. / Gentili, H. / Rodriguez, N.A. / Aran, M. / Hermoso, J.A. / Ibanez, L.I. / Santos, J.
History
DepositionDec 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 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: Frataxin mature form
C: Camelid Nanobody 6B1


Theoretical massNumber of molelcules
Total (without water)26,5852
Polymers26,5852
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.253, 97.253, 128.105
Angle α, β, γ (deg.)90, 90, 120
Int Tables number182
Space group name H-MP6322
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11C-305-

HOH

21C-306-

HOH

31C-309-

HOH

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Components

#1: Protein Frataxin mature form / Frataxin(81-210) / m81-FXN


Mass: 12758.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FXN, FRDA, X25 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16595
#2: Antibody Camelid Nanobody 6B1


Mass: 13827.233 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 59.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.0 0.8M Potassium Sodium Tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.48→84.224 Å / Num. obs: 50815 / % possible obs: 96.8 % / Redundancy: 20.5 % / Biso Wilson estimate: 27.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 33.5
Reflection shellResolution: 1.485→1.584 Å / Redundancy: 21.7 % / Num. unique obs: 2541 / CC1/2: 0.571 / % possible all: 74.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→84.224 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.159 / SU B: 3.292 / SU ML: 0.048 / Average fsc free: 0.9806 / Average fsc work: 0.9887 / Cross valid method: FREE R-VALUE / ESU R: 0.096 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1753 1728 4.784 %
Rwork0.1509 34396 -
all0.152 --
obs-36124 99.983 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.057 Å2
Baniso -1Baniso -2Baniso -3
1--0.545 Å2-0.272 Å2-0 Å2
2---0.545 Å20 Å2
3---1.767 Å2
Refinement stepCycle: LAST / Resolution: 1.76→84.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 0 153 2028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0161939
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161747
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.7772638
X-RAY DIFFRACTIONr_angle_other_deg0.51.5654034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3125.179251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98410301
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.3781086
X-RAY DIFFRACTIONr_chiral_restr0.0810.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02457
X-RAY DIFFRACTIONr_nbd_refined0.20.2335
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21535
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2968
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21104
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2133
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1670.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2450.24
X-RAY DIFFRACTIONr_nbd_other0.2240.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1070.216
X-RAY DIFFRACTIONr_mcbond_it8.7022.082971
X-RAY DIFFRACTIONr_mcbond_other8.6792.081971
X-RAY DIFFRACTIONr_mcangle_it11.5973.7351212
X-RAY DIFFRACTIONr_mcangle_other11.6283.7381213
X-RAY DIFFRACTIONr_scbond_it11.7832.509968
X-RAY DIFFRACTIONr_scbond_other11.7782.51968
X-RAY DIFFRACTIONr_scangle_it16.0054.4161426
X-RAY DIFFRACTIONr_scangle_other15.9994.4171427
X-RAY DIFFRACTIONr_lrange_it21.0923.1082235
X-RAY DIFFRACTIONr_lrange_other20.69822.4912192
X-RAY DIFFRACTIONr_rigid_bond_restr3.38833686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.76-1.8060.1631200.13225210.13426410.9830.991000.104
1.806-1.8550.1571070.11724370.11925440.990.9931000.093
1.855-1.9090.1761220.12423510.12724730.980.9911000.098
1.909-1.9680.1641090.1122980.11324080.9850.99399.95850.088
1.968-2.0320.1671190.11222330.11523520.9840.9931000.091
2.032-2.1030.1731160.11421410.11722570.9820.9921000.096
2.103-2.1830.1931000.11921010.12222010.9810.9921000.102
2.183-2.2720.155990.11920200.12121190.9850.9921000.104
2.272-2.3730.1761040.12919420.13120460.9770.9911000.116
2.373-2.4880.246960.14818480.15319440.9590.9871000.139
2.488-2.6230.197830.15117770.15418600.9740.9861000.145
2.623-2.7820.173750.15916920.1617670.9770.9841000.158
2.782-2.9740.222780.1615890.16316670.970.9841000.166
2.974-3.2120.166810.16614830.16615650.9870.98499.93610.175
3.212-3.5180.155690.16513690.16414380.9880.9851000.18
3.518-3.9320.174640.15112630.15213270.9810.9861000.171
3.932-4.5390.146580.13611100.13711680.9870.9891000.169
4.539-5.5550.163610.1389660.1410270.9880.991000.171
5.555-7.8380.229400.2177720.2178130.9750.97699.8770.276
7.838-84.2240.165260.2494800.2445090.9770.94999.41060.357
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)
15.97220.74380.38731.2548-0.03292.04380.0632-0.64550.12920.1921-0.08620.3247-0.0024-0.69870.0230.1062-0.04330.00670.378-0.06370.14959.905-38.05716.391
21.7273-0.1322-0.01081.71280.77332.4547-0.0050.0019-0.13060.0061-0.05360.06250.3089-0.06420.05850.0467-0.01280.00850.0246-0.01230.016439.422-39.16113.263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA4 - 114
2X-RAY DIFFRACTION2ALLC2 - 128

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