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- PDB-9ho6: Crystal Structure of the Human Frataxin protein in complex with a... -

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Basic information

Entry
Database: PDB / ID: 9ho6
TitleCrystal Structure of the Human Frataxin protein in complex with a tailored Camelid Nanobody 16C10
Components
  • Camelid Nanobody 16C10
  • 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: 2 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
D: Camelid Nanobody 16C10
B: Frataxin mature form
C: Camelid Nanobody 16C10


Theoretical massNumber of molelcules
Total (without water)57,5464
Polymers57,5464
Non-polymers00
Water4,234235
1
A: Frataxin mature form
C: Camelid Nanobody 16C10


Theoretical massNumber of molelcules
Total (without water)28,7732
Polymers28,7732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-4 kcal/mol
Surface area11700 Å2
2
D: Camelid Nanobody 16C10
B: Frataxin mature form


Theoretical massNumber of molelcules
Total (without water)28,7732
Polymers28,7732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-4 kcal/mol
Surface area11470 Å2
Unit cell
Length a, b, c (Å)57.899, 81.100, 107.546
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 13619.087 Da / Num. of mol.: 2
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 16C10


Mass: 15153.678 Da / Num. of mol.: 2
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.: 235 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 15% PEG 10K 0.1M Ammonium acetate 0.1M Bis-Tris pH 5.5

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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: Jul 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.997→64.752 Å / Num. obs: 25980 / % possible obs: 91.7 % / Redundancy: 11.5 % / Biso Wilson estimate: 28.76 Å2 / CC1/2: 0.997 / Net I/σ(I): 14.2
Reflection shellResolution: 1.997→2.183 Å / Num. unique obs: 1299 / CC1/2: 0.39

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_4958refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→64.75 Å / SU ML: 0.2208 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.6836
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2274 1327 5.11 %
Rwork0.1799 24650 -
obs0.1824 25977 74.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.28 Å2
Refinement stepCycle: LAST / Resolution: 2→64.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3754 0 0 235 3989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073858
X-RAY DIFFRACTIONf_angle_d0.99595246
X-RAY DIFFRACTIONf_chiral_restr0.0535580
X-RAY DIFFRACTIONf_plane_restr0.0116680
X-RAY DIFFRACTIONf_dihedral_angle_d17.20191386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.080.283640.2833124X-RAY DIFFRACTION3.34
2.08-2.170.3406450.2563932X-RAY DIFFRACTION25.66
2.17-2.290.3351950.24921699X-RAY DIFFRACTION46.51
2.29-2.430.23941870.23463178X-RAY DIFFRACTION87.2
2.43-2.620.26361830.2223686X-RAY DIFFRACTION99.67
2.62-2.880.29272060.20993658X-RAY DIFFRACTION99.97
2.88-3.30.24791790.19183736X-RAY DIFFRACTION99.97
3.3-4.150.2012190.15183735X-RAY DIFFRACTION100
4.15-64.750.18522090.14663902X-RAY DIFFRACTION99.95
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)
11.25843273279-0.391125609115-0.2043594445291.35029059653-0.1126754718281.30827698824-0.138246703306-0.02735014374870.228742073736-0.1259588219280.0778850800656-0.05655842835-0.1099245668690.0113334690334-0.002771189302990.225203885921-0.0443940642595-0.1088762536470.1948329612850.0149608254460.28315177172537.52466496346.468492108953.48407665205
21.40573516860.7960687578640.3035410844751.618903255050.5827350232611.72338241996-0.2691728664780.05328582377490.324807728105-0.2215761002770.05947577151470.182258923154-0.2357255556220.00419870442785-0.01408261686660.222027581920.0105099945952-0.08123976889780.157069577886-0.01303608289780.2201619288777.4260905252-1.94630716448-2.49548831119
31.169977003650.448214868739-0.5124367457881.478777145280.2263163785891.83094244837-0.0558976089237-0.16437511430.08383503178280.0351557605785-0.0426828006763-0.05179224595350.181861632920.168264346661-0.01743802584690.1364685694430.0685837582340.02335696282490.226938277874-0.04634883334030.1558672215998.93377415449-13.431273308425.9570431956
41.663207228370.147235773594-0.5060397512731.811023142680.2705033050771.81769093047-0.212709526317-0.2140583603870.01491568829360.2082785250130.1509807715270.08508561294490.1870987733460.0398427123281-0.002438694374760.2345893007790.066953057224-0.01700304205280.202687823508-0.01648527855470.15752508151239.2282574942-20.236001641418.6231109055
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 1:121)AA1 - 1211 - 121
22(chain D and resseq 1:123)DB1 - 1231 - 123
33(chain B and resseq 1:121)BC1 - 1211 - 121
44(chain C and resseq 1:123)CD1 - 1231 - 123

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