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- PDB-32je: Nanobody Nb1 against SOG1 NAC domain -

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Basic information

Entry
Database: PDB / ID: 32je
TitleNanobody Nb1 against SOG1 NAC domain
ComponentsNanobody Nb1 against SOG1 NAC domain
KeywordsIMMUNE SYSTEM / Nanobody / SOG1 / DNA Damage Response
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Mignon, K. / Van Den Haute, L. / 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

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Assembly

Deposited unit
A: Nanobody Nb1 against SOG1 NAC domain
B: Nanobody Nb1 against SOG1 NAC domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,38410
Polymers31,9792
Non-polymers4058
Water2,018112
1
A: Nanobody Nb1 against SOG1 NAC domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1925
Polymers15,9901
Non-polymers2024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nanobody Nb1 against SOG1 NAC domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1925
Polymers15,9901
Non-polymers2024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.658, 92.152, 61.489
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 1 through 85 or resid 87...
d_2ens_1(chain "B" and (resid 1 through 19 or (resid 20...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETASNASNAA1 - 851 - 85
d_12LEULEUSERSERAA87 - 12787 - 127
d_21METMETASNASNBB1 - 851 - 85
d_22LEULEUSERSERBB87 - 12787 - 127

NCS oper: (Code: givenMatrix: (-0.999939710711, -0.0102658225332, 0.00389715668326), (-0.00274200841297, 0.577109487654, 0.816662182698), (-0.010632795134, 0.81660226068, -0.577102843105)Vector: 22. ...NCS oper: (Code: given
Matrix: (-0.999939710711, -0.0102658225332, 0.00389715668326), (-0.00274200841297, 0.577109487654, 0.816662182698), (-0.010632795134, 0.81660226068, -0.577102843105)
Vector: 22.1823666067, -7.5490256807, 20.1112220729)

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Components

#1: Antibody Nanobody Nb1 against SOG1 NAC domain


Mass: 15989.641 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Na-HEPES pH 7.5, 2% v/v PEG-400, 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: 0.978564 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978564 Å / Relative weight: 1
ReflectionResolution: 2.3→45.06 Å / Num. obs: 13474 / % possible obs: 98.9 % / Redundancy: 5.24 % / Biso Wilson estimate: 33.24 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.255 / Rrim(I) all: 0.281 / Net I/σ(I): 5.16
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 5.36 % / Rmerge(I) obs: 1.163 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 2141 / CC1/2: 0.498 / Rrim(I) all: 1.286 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.06 Å / SU ML: 0.3314 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.5098
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2732 674 5.01 %
Rwork0.2074 12768 -
obs0.2107 13442 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 16 112 1993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781921
X-RAY DIFFRACTIONf_angle_d0.94222614
X-RAY DIFFRACTIONf_chiral_restr0.0599287
X-RAY DIFFRACTIONf_plane_restr0.0071335
X-RAY DIFFRACTIONf_dihedral_angle_d12.9103658
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.377793622838 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.34521320.2762509X-RAY DIFFRACTION99.59
2.48-2.730.3611330.25752522X-RAY DIFFRACTION99.48
2.73-3.120.28711340.22982537X-RAY DIFFRACTION99.63
3.12-3.930.24171350.18242560X-RAY DIFFRACTION98.94
3.93-45.060.24581400.18392640X-RAY DIFFRACTION97.51
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)
16.46183391339-3.455347273886.052824957762.32737206682-3.100792697355.627972314830.157956530528-0.9425583370190.7998285605440.423885199001-0.200654187955-0.4660124881690.101771100894-0.2281141344790.360585258660.340365195381-0.0618776154790.02391217381180.307360104973-0.01419634567990.5028335529722.89219949417-11.2318329417-5.8234792125
27.71162550403-0.436780405973-3.625090668391.05631718017-1.297200389547.429300179460.193879582149-0.802000241168-0.502474182122-0.273277950339-0.8832415739040.01648706276710.828842942210.6717707910940.3360641606070.337330291971-0.100155148527-0.09494874850940.3075759697280.07700671434350.46203510396921.724049678-10.98825959978.15399704549
34.490987189371.639841761833.467988239890.9415431813331.65663539942.994710257040.236386173169-0.0491970095149-0.4650137619440.149645560905-0.07382915446550.09964514151460.546996055524-0.200036366005-0.1499994835150.273814451646-0.02126441074850.05650019786520.2903782148160.04329877400920.2677302703227.43627880207-15.7623992129-10.1420253982
41.416806157562.026224920751.578241614182.999677918952.936850245264.357460542230.40441432484-0.1408594307390.08538749867741.50577271625-0.0166874381316-0.5094753718590.9702675662360.00497381457952-0.194397766830.361093847194-0.00449733769492-0.08782523211820.2992230321790.00207453329720.2970619529115.7836744605-2.62576264588-5.97081330122
56.657927245354.50796230428-0.879305209078.115758538853.296044730576.85550106836-0.5011895448650.522480885457-0.292688824294-0.6346025838990.73085714015-0.233416526908-0.615697172370.40686241265-0.207769920670.2761302329210.00859629932283-0.01359936780630.2936778645760.04458257250040.26541925643919.1166701968-12.6897439142-14.2350153713
68.771251214164.503874629432.024189458397.300079922021.895074431813.772737726010.2036484983-0.31111761369-0.593892145677-0.209022098971-0.132294423743-0.854633681490.07065429456690.151976658957-0.1887814448070.2820145892480.0424943300112-0.007107190041760.263393060924-0.006419560889350.33879720674222.7833446338-13.096611449-7.76489577628
71.907746058960.5379937104750.9103929313670.4300563139130.6535256781554.24600557360.0948266466151-0.18350524406-0.1021213747080.231864662282-0.0191555986575-0.101339827158-0.2062010824530.20256351935-0.06183719110860.262748002841-0.02391420541-0.0036979560520.2291940011470.01253558746410.27724789654516.4423241-11.5000441526-3.87666288101
83.5612987676-3.26130912735-0.9554048232446.03893536923-2.433019251124.408561073760.09803784564291.18629047812-0.0378090583909-0.9990194083390.253702646278-0.2397139383230.188743477548-0.0534104843101-0.02598703737420.3637566896130.0757603102134-0.03261076692540.375531049901-0.006727334425060.52870581541614.2260118526-9.28701647578-20.9666413438
91.72962774393-2.20011948573-0.0005069868683162.78503256102-0.3355010019912.43466436261-0.188062162657-0.1129274049620.2697365698040.345154522391-0.08369597447530.1383618210450.295490705016-0.4384406965330.4470431900070.225609615654-0.108507434601-0.05955371047010.345099943509-0.03303189951950.378825040411.7332706096-5.58860899335-3.51511366866
105.27052396194-5.157353608233.950173114699.03452354916-4.9002415267.03398576462-0.3021389258850.1686023589590.6837284387810.2554862539440.1435205916580.337650535659-0.2935613780170.03554595286270.05433166994040.3125955343530.0093758786210.05133358279830.363407138968-0.03721896837080.38748881216719.3028817947-18.828018474514.1875925069
113.33257068613-1.49593442087-1.754886936171.176487866441.288269188174.733615422610.8461665222390.8666000167942.0938302305-1.57098369602-0.413870068031-0.398141962211-0.398167755884-0.149014316476-0.3515527397640.4054002293790.06186528158010.04081590343080.2888190083230.04827116865070.6556001038820.749415715931-7.254727797386.17328182897
128.76494816461-3.540927998156.961262518712.96248655939-5.20203623079.202307370710.4000015022321.461167827350.826303700924-0.36990892553-0.603378457513-0.06455979083870.5369298516090.6936759618590.5064134208330.235889497755-0.0157250290326-0.04250266829410.3649531864090.03338288248740.39727643882811.5222693283-18.91419524978.88175036826
131.17112223710.852785836873-0.2589104155292.080608433050.8303379855451.113282340180.0318619843809-0.121322156125-0.111339588141-0.265276957809-0.06102075754050.118107769244-0.1873103214320.1837044304510.0002603551706760.250349052116-0.0219745051131-0.01555833841770.2833535766960.06329242523090.26311191326410.8074908289-20.514776743219.0510793437
143.27102273918-2.65616863822-1.522756111887.527564522722.066458916362.870221407210.1986166295940.17313500958-0.470535932795-0.113218656174-0.4615951012421.09555845004-0.18882991518-0.1011538621120.1526104662650.273393234911-0.006224397528-0.02374247998170.254631528752-0.00498585231710.3274574047163.16473135277-26.537400346917.80830291
153.63829545708-1.05506351496-1.290280564582.657317457190.8176995572161.419384278720.2268025192320.234819503420.109318084734-0.145101545644-0.1993962649360.369823023921-0.219675671486-0.2708449701110.009235559649470.2932376912860.0479845191714-0.03956662361140.292672538469-0.04198335231270.4264394113583.83773670834-22.411208065211.3936653877
165.270778638192.262844788242.004090267912.121868561011.429587826988.804404233280.49626709035-0.30541379461-0.2867732479720.10428177768-0.06459840086270.561736528164-0.818832735231-0.914969367797-0.5027478318470.3409891756040.04349650123430.0279188855060.2917586270310.0259784987460.57869670953-3.57389498878-10.075631324912.2295137358
175.80040029013-4.781135418243.143133437624.38073238953-3.768597055025.302881927430.6523465355060.294414958184-0.276281536594-0.747531097833-0.9005575425040.1030031106020.3622968567860.4025546860080.4224269769690.2796336656770.0004961844119630.01183895175430.250323633910.01876326470860.46147325105110.490257298-17.053827393918.5965222801
182.5582910622-3.41835073383-1.136413273275.726138703420.1342386996135.43214992631-0.0579838751050.132231267592-0.8025320976060.2154510506690.0009414669759790.4879035004430.654147281897-0.05634230827840.11363093180.398560275906-0.03620808868480.07924030325220.4230059746180.01499513192460.4603677459017.81373713933-30.195442407924.2965213932
195.36606959189-3.993357540462.881293551857.60124731136-3.840055676973.7919794318-0.0419091804275-0.4663609015350.9066509551440.441598248436-0.234434592339-0.854612586135-0.205796828464-0.02665952121590.1887724826440.368683793430.0140473345414-0.03047592613030.309053674234-0.04361716388370.30316448625110.5813373765-13.703988086817.481707761
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 8 )AA1 - 81 - 8
22chain 'A' and (resid 9 through 18 )AA9 - 189 - 18
33chain 'A' and (resid 19 through 34 )AA19 - 3419 - 34
44chain 'A' and (resid 35 through 46 )AA35 - 4635 - 46
55chain 'A' and (resid 47 through 61 )AA47 - 6147 - 61
66chain 'A' and (resid 62 through 74 )AA62 - 7462 - 74
77chain 'A' and (resid 75 through 100 )AA75 - 10075 - 100
88chain 'A' and (resid 101 through 114 )AA101 - 114101 - 114
99chain 'A' and (resid 115 through 127 )AA115 - 127115 - 127
1010chain 'B' and (resid 1 through 8 )BB1 - 81 - 8
1111chain 'B' and (resid 9 through 18 )BB9 - 189 - 18
1212chain 'B' and (resid 19 through 26 )BB19 - 2619 - 26
1313chain 'B' and (resid 27 through 46 )BB27 - 4627 - 46
1414chain 'B' and (resid 47 through 61 )BB47 - 6147 - 61
1515chain 'B' and (resid 62 through 84 )BB62 - 8462 - 84
1616chain 'B' and (resid 85 through 92 )BB85 - 9285 - 92
1717chain 'B' and (resid 93 through 100 )BB93 - 10093 - 100
1818chain 'B' and (resid 101 through 114 )BB101 - 114101 - 114
1919chain 'B' and (resid 115 through 127 )BB115 - 127115 - 127

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