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- PDB-32jh: Nanobody Nb7 against SOG1 NAC domain -

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Basic information

Entry
Database: PDB / ID: 32jh
TitleNanobody Nb7 against SOG1 NAC domain
ComponentsNanobody Nb7 against SOG1 NAC domain
KeywordsIMMUNE SYSTEM / Nanobody / SOG1 / DNA Damage Response
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLoris, R. / Van Den Haute, L. / Mignon, K.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1103622N Belgium
CitationJournal: To Be Published
Title: A nanobody and megabody toolbox for SOG1, the central regulator of the plant DNA damage response
Authors: Van Den Haute, L. / Mignon, K. / Van der Eecken, R. / Fislage, M. / Pardon, E. / Steyaert, J. / Loris, R.
History
DepositionJul 12, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nanobody Nb7 against SOG1 NAC domain
B: Nanobody Nb7 against SOG1 NAC domain
C: Nanobody Nb7 against SOG1 NAC domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,51611
Polymers47,9903
Non-polymers5268
Water1,00956
1
A: Nanobody Nb7 against SOG1 NAC domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2854
Polymers15,9971
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nanobody Nb7 against SOG1 NAC domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1283
Polymers15,9971
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nanobody Nb7 against SOG1 NAC domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1034
Polymers15,9971
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.017, 67.656, 55.505
Angle α, β, γ (deg.)90.000, 90.590, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and ((resid 3 and (name N or name...
d_2ens_1(chain "B" and ((resid 3 and (name N or name...
d_3ens_1(chain "C" and (resid 3 through 13 or (resid 14...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 3 - 125 / Label seq-ID: 4 - 126

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC

NCS oper:
IDCodeMatrixVector
1given(0.540519062268, 0.840956866412, 0.025113585158), (0.840857274314, -0.540975865661, 0.0174400976458), (0.0282522133368, 0.0116902355388, -0.999532466123)-15.4156789342, 26.3356011074, 72.678198979
2given(-0.485283192494, 0.87428449303, -0.0112626964108), (-0.874355341336, -0.485216644756, 0.00821856008578), (0.00172051187469, 0.0138359278407, 0.999902798746)42.291701224, 56.3067026445, 18.2835900562

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Components

#1: Antibody Nanobody Nb7 against SOG1 NAC domain


Mass: 15996.573 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M Na-acetate pH 4.6 2.0 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.45→40.1 Å / Num. obs: 8645 / % possible obs: 54.7 % / Redundancy: 4.28 % / Biso Wilson estimate: 24.28 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.186 / Rrim(I) all: 0.211 / Net I/σ(I): 4.58
Reflection shellResolution: 2.45→2.8 Å / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 1080 / CC1/2: 0.9242 / Rrim(I) all: 0.586 / % possible all: 21

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→40.1 Å / SU ML: 0.4606 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.752
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3282 375 4.34 %
Rwork0.2628 8260 -
obs0.2656 8635 54.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.06 Å2
Refinement stepCycle: LAST / Resolution: 2.45→40.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 24 56 2757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00962747
X-RAY DIFFRACTIONf_angle_d1.24333735
X-RAY DIFFRACTIONf_chiral_restr0.067403
X-RAY DIFFRACTIONf_plane_restr0.0117493
X-RAY DIFFRACTIONf_dihedral_angle_d17.3482907
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.821884032174
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.692987235157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.80.3387610.35621041X-RAY DIFFRACTION21.05
2.81-3.530.37861250.28512506X-RAY DIFFRACTION50.26
3.53-40.10.3021890.24414713X-RAY DIFFRACTION92.06
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)
12.917038637951.6761183433-0.7167782968372.873855146590.03208313271892.677231924990.13898491108-0.191501293672-0.5187663230850.241456135402-0.18896571363-0.3088340382610.3582136597910.05800107584520.009293047752510.357921925322-0.184157156247-0.08351311556920.2441492645290.1072669816570.35987324314520.727916609411.193820205528.7666034027
21.29245403291-0.3384124297620.5581290143580.654689420427-0.4653940708851.206792233720.1048836636250.0900115161508-0.152869090719-0.07236543631340.1964398976690.320856164296-0.130684400798-0.369367172895-0.08447092612370.2623958928550.1138090300220.143482111210.3000357961770.04791140291170.13993821836521.961772370721.305979765728.5904837794
30.625347484944-0.00916756845911-0.1471333909490.746677633851-0.06326397712491.698156059350.072313634422-0.0506469884727-0.0963144818735-0.215638315553-0.0599347697593-0.006778589880160.01557908474030.140643160002-0.02843712214060.2279147063670.0244047673265-0.02740178249370.203381912590.04746598067860.1930386092926.363721074425.724875642229.2063575633
40.319731607611-0.06469366629580.06357749010260.483768636449-0.3601416894960.291614906381-0.06001407662930.09283236769550.172369464785-0.315157524969-0.0552747598579-0.00888554827068-0.294642488644-0.003003197996920.1250676921590.4036060041970.0616621747171-0.08604264097670.1293471473480.01176404030590.20365588998626.974424764721.403011029824.1119009117
50.00343939159355-0.002442694318950.01072672766470.648638679875-0.2243269124620.119125241740.0142549758248-0.143723006559-0.04047818691030.05888582965540.06768035522030.1318727875180.138145107675-0.0430327667676-0.03790838885730.4270145114410.169971028953-0.183983199530.3491500760530.01270090390160.40209369398813.480996829827.004442569847.9436079757
60.0939998570388-0.102684316565-0.02763589042170.442106550508-0.1580537313060.1194645783840.0952557520517-0.02525458611-0.10344450555-0.1209792921190.06394590246540.1463593874970.1331045129340.0439418685658-0.03667421550080.06457539620540.2847997555-0.3261168466040.4670801046710.233343953971-0.31437255427518.53837916737.063112054246.207309213
70.584521215473-0.418698414085-0.09564691931981.616178680780.08023957597351.16677848827-0.05153710867450.137577011650.1445414803460.0168539571084-0.0298584299447-0.0114707532016-0.1069376971380.0968498905860.02874517715440.2988936715650.01635497563070.1147815735480.335835645180.07387924455670.5235146711454.669315269831.544399014643.624901363
80.6369423092950.586083327545-0.1117231197211.01044930396-0.2444467916460.06114749500760.0573532728775-0.07262742500910.199211925999-0.00161755112627-0.04213060106740.0504489365267-0.1131633218880.0774268489225-0.107884459440.130509299459-0.1078568947580.1527609164780.23560817574-0.2158207903960.33610805978344.390846296427.278943633452.7732583797
91.268042691520.182989959986-0.02378090293510.5814059971290.2433533242710.249019449489-0.01688153061490.1782531484030.113701242124-0.138168545225-0.08077776455430.0481903567408-0.07166981004660.206904149097-0.08070960698660.1422739315640.07511826579630.02020545796790.3856929571130.02434825304670.14090692272649.544108181221.979838784645.0721880407
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 7 )AA1 - 71 - 7
22chain 'A' and (resid 8 through 39 )AA8 - 398 - 39
33chain 'A' and (resid 40 through 83 )AA40 - 8340 - 83
44chain 'A' and (resid 84 through 125 )AA84 - 12584 - 125
55chain 'B' and (resid 3 through 20 )BB3 - 201 - 18
66chain 'B' and (resid 21 through 125 )BB21 - 12519 - 123
77chain 'C' and (resid 2 through 17 )CC2 - 171 - 16
88chain 'C' and (resid 18 through 33 )CC18 - 3317 - 32
99chain 'C' and (resid 34 through 126 )CC34 - 12633 - 125

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