PDB-32jg: Nanobody Nb3 against SOG1 NAC domain

ID or keywords:

Entry

Database: PDB / ID: 32jg

Title

Nanobody Nb3 against SOG1 NAC domain

Components

Nanobody Nb3 against SOG1 NAC domain

Keywords

IMMUNE SYSTEM / Nanobody / SOG1 / DNA Damage Response

Function / homology

CITRATE ANION

Function and homology information

Biological species

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Loris, R. / Van Den Haute, L. / Mignon, K.

Funding support

Belgium, 1items

Citation

Journal: 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

Deposition	Jul 12, 2026	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 26, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	32jg.cif.gz	142.8 KB	Display	PDBx/mmCIF format
PDB format	pdb32jg.ent.gz	91.7 KB	Display	PDB format
PDBx/mmJSON format	32jg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/2j/32jg ftp://data.pdbj.org/pub/pdb/validation_reports/2j/32jg	HTTPS FTP

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Related structure data

Related structure data	32jeC 32jhC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#136 - Apr 2011
Nanobodies
similarity (1)
#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#129 - Sep 2010
Isocitrate Dehydrogenase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#191 - Nov 2015
Glutamate-gated Chloride Receptors
similarity (1)
#215 - Nov 2017
Aspartate Transcarbamoylase
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)

Deposited unit

A: Nanobody Nb3 against SOG1 NAC domain

B: Nanobody Nb3 against SOG1 NAC domain

hetero molecules

31.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Nanobody Nb3 against SOG1 NAC domain

hetero molecules

defined by author
Evidence: gel filtration
15.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Nanobody Nb3 against SOG1 NAC domain

hetero molecules

defined by author
Evidence: gel filtration
16 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	40.780, 66.480, 97.500
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁
Space group name Hall	P22ab(z,x,y)
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y+1/2,-z+1/2 #4: -x,-y+1/2,z+1/2

#1: Antibody	Nanobody Nb3 against SOG1 NAC domain Mass: 15818.515 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-FLC / CITRATE ANION Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₅O₇
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 41.36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M Na-citrate pH 5.6, 20% v/v 2-Propanol, 20% w/v PEG4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2026
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.45→39.31 Å / Num. obs: 46347 / % possible obs: 96.9 % / Redundancy: 12.59 % / B_iso Wilson estimate: 24.01 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.084 / R_rim(I) all: 0.087 / Net I/σ(I): 13.63
Reflection shell	Resolution: 1.45→1.54 Å / Redundancy: 8.69 % / R_merge(I) obs: 2.155 / Mean I/σ(I) obs: 0.72 / Num. unique obs: 6246 / CC_1/2: 0.363 / R_rim(I) all: 2.288 / % possible all: 82.3

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Processing

Software

Name	Version	Classification
PHENIX	1.21.1_5286	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.45→39.31 Å / SU ML: 0.2402 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.6011
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2186	2315	5 %
R_work	0.1851	43979	-
obs	0.1867	46294	96.78 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 33.57 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→39.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1862	0	19	246	2127

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0044	2030
X-RAY DIFFRACTION	f_angle_d	0.7776	2782
X-RAY DIFFRACTION	f_chiral_restr	0.0766	296
X-RAY DIFFRACTION	f_plane_restr	0.0055	369
X-RAY DIFFRACTION	f_dihedral_angle_d	12.8219	746

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.45-1.48	0.5227	102	0.5235	1942	X-RAY DIFFRACTION	73.98
1.48-1.51	0.4972	115	0.4563	2177	X-RAY DIFFRACTION	82.56
1.51-1.55	0.4103	128	0.4253	2447	X-RAY DIFFRACTION	93.23
1.55-1.59	0.3757	136	0.3564	2567	X-RAY DIFFRACTION	97.44
1.59-1.63	0.3309	139	0.3016	2656	X-RAY DIFFRACTION	99.86
1.63-1.68	0.3001	138	0.285	2618	X-RAY DIFFRACTION	99.71
1.68-1.73	0.3148	138	0.2559	2630	X-RAY DIFFRACTION	99.71
1.73-1.79	0.2509	139	0.23	2634	X-RAY DIFFRACTION	99.6
1.79-1.86	0.1981	140	0.1893	2665	X-RAY DIFFRACTION	99.82
1.86-1.95	0.2285	140	0.1719	2647	X-RAY DIFFRACTION	99.68
1.95-2.05	0.2021	140	0.168	2662	X-RAY DIFFRACTION	99.86
2.05-2.18	0.1831	139	0.1693	2637	X-RAY DIFFRACTION	99.86
2.18-2.35	0.1994	142	0.1742	2690	X-RAY DIFFRACTION	99.93
2.35-2.58	0.2283	141	0.1898	2686	X-RAY DIFFRACTION	99.86
2.58-2.96	0.2167	143	0.186	2713	X-RAY DIFFRACTION	99.96
2.96-3.73	0.2137	145	0.1597	2740	X-RAY DIFFRACTION	99.83
3.73-39.31	0.1757	150	0.1494	2868	X-RAY DIFFRACTION	99.64

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.84595127344	-0.163417118607	0.0170169008407	2.44198460834	-0.909993533073	6.88683040551	0.276003578741	0.441120385761	-0.206378261439	-0.277345407373	-0.0103962503982	0.148153476609	0.333679605352	0.283705464399	-0.245920547997	0.192467561404	-0.0192367196674	-0.00364511899032	0.2405638226	-0.0540831805049	0.226062743216	5.03864977253	9.85863258767	13.1588706938
2	2.34644939518	-0.893588709341	-0.245058344066	1.92750671718	-1.56666294875	6.71317100216	-0.0377060785081	-0.158811655395	-0.441801876423	0.0471308608733	0.236980353779	0.130621892973	0.454364796078	-0.133296866849	-0.249407642449	0.243596168438	0.0106483624552	-0.00253198525496	0.226093317341	0.0128881481344	0.306412248487	5.16970053154	5.80404281733	26.0973112877
3	2.92371624175	-0.951367806582	-0.130352895404	4.40201958305	-3.24223078402	7.01562131082	0.0244761534297	0.101006169434	0.325460888714	-0.13706276667	-0.0662668823655	-0.457456387633	-0.611717732718	0.380662872521	-0.0212499320045	0.320900730637	-0.0290870677474	0.0324725039934	0.305704018937	-0.0308705672416	0.289094758981	8.52550908056	19.3246292368	19.4190298411
4	5.46535350923	-0.828784312879	-1.56714461094	2.8628217113	1.50755042394	5.81413090538	-0.105525336949	-0.268370654708	0.0399653657257	0.222003922067	0.167068462231	-0.0477162032429	-0.0978635640244	0.117299387374	-0.0886442905169	0.236897236146	0.0223709192433	0.0086975095401	0.231717324577	-0.0114503820104	0.207165205812	-0.0540963037834	16.8764752854	28.1043613279
5	7.2041686731	-2.28631001913	0.0683797665502	1.09778913658	1.46977507705	6.03037185658	-0.079777314353	0.347604510649	0.760723578467	0.383799036718	0.00748338143567	0.945944878826	-2.20453818254	-0.895499852076	-0.0760483779223	0.577929787396	0.210154577739	0.108088607217	0.345990596748	0.0299835806882	0.325971826391	-4.15632171628	22.7874271933	18.4089177857
6	4.57945537347	-0.350612960494	-0.338097091257	1.98087437893	-0.620873301638	6.39432568885	0.0247959125959	0.063886462144	-0.466760460143	0.0577176819429	0.0984530710998	0.268313985377	0.446094450711	0.00657431745907	-0.191592991207	0.252661601884	-0.00590964163586	-0.0083913354159	0.199091272257	-0.0137953797985	0.312634815834	-1.1767761701	7.74122331352	23.0279264966
7	4.03361773097	-0.363184555956	0.27320219632	1.40889113078	-0.685867020003	6.73190059024	0.0553592523689	0.44288187627	0.246148795468	0.0232604828646	0.0635615598306	0.0462045953048	-0.407845361123	-0.0706132604629	-0.173050910256	0.241606439621	0.0038548851419	0.0106821129968	0.25142372234	-0.0121342826212	0.227278138024	3.36223213557	18.0775332394	14.3478878073
8	4.9039784568	-0.763847204888	-2.53958930279	1.97697281472	0.0547695957922	5.07408646618	-0.582129449395	-1.37221862568	0.341809574921	1.03040738904	0.694432008519	0.0315652713552	-0.464855905514	-0.222042083294	-0.143118836506	0.412102876946	0.112004026038	0.0466227264689	0.643090029482	-0.00305722824505	0.261589287424	4.08940776424	15.4982249123	37.1776672776
9	5.20670308985	-0.241897461642	1.29865126187	2.64186456096	1.40257030102	8.65332053315	0.0305277625844	-0.226700706798	0.201072990542	0.179291492726	0.206786540517	-0.242325767086	0.0937241187868	0.118574650071	-0.29681825895	0.214856491415	-0.00985195458176	-0.0176501288358	0.278133548651	-0.027739978482	0.25264426127	12.764433317	14.9991054915	26.648745028
10	1.25706645706	-0.0423391611793	-1.78850628294	0.501588229524	0.295781803726	2.65457661595	0.59089207992	0.646635238129	-0.355506105681	-0.372106585393	-0.12791244872	0.356696334295	-0.127857830092	0.147282520363	-0.322144681771	0.303659253941	0.0240104416939	0.00803092043435	0.372012610733	-0.00447145904549	0.243329166816	4.23972390587	16.8073972137	5.61775625697
11	4.91903996768	-0.0729152938599	1.80989544911	1.3485354819	1.60786602157	5.82838754651	0.251766568817	-0.5906207264	-0.199392800403	0.284262456104	-0.0549090906274	-0.0782950956457	0.47983818316	-0.0546905963647	-0.339800571208	0.250074650328	-0.00844506580462	-0.0126601306442	0.285901371358	0.055020197459	0.225987327456	15.0092709732	9.09175707983	0.37556882572
12	1.99989582922	1.27367731387	0.148703009128	2.72948438408	2.06469458652	6.50392344762	0.0372466461989	-0.130497668146	-0.0478639083791	0.027481934945	-0.0559748822908	0.020100626525	-0.118492067687	0.0754364139715	-0.0360796539914	0.173843195874	0.0195327621398	-0.00200482402447	0.205146044961	0.00830058715757	0.213951255155	14.304208028	10.2498184478	-9.17465108241
13	2.25674231155	-2.93673847076	-2.21256148641	7.04426621638	2.41653530059	2.22984350001	0.0509334369947	-0.168727253126	0.275353665773	0.0170489670695	0.164683866127	0.0156450016566	-0.508782852439	0.241840965381	-0.0546720212739	0.279065475392	0.0126805964937	0.00750528535706	0.280869426093	0.0102164374324	0.261837716117	15.8968166865	18.997591015	-10.2389070467
14	7.0875254819	2.05167476158	-1.11774965862	5.98113030064	2.22357077698	2.81977082931	-0.0265987418926	0.00132613426501	0.33046004779	-0.0430408342398	0.0424878062389	0.0755798932743	-0.363454878663	0.484863943478	-0.013548393654	0.29161378213	-0.0227354371786	0.033426639389	0.254581237928	0.0165367416114	0.211899111846	23.0137226281	16.2793186668	-14.7765146514
15	4.09084208593	-0.631068442991	-0.340383302625	2.432059702	2.55997578936	6.2188797898	0.0970653204882	-0.0170478711599	-0.0840786729509	0.120464385445	0.146188664189	-0.298897516848	0.203694307968	0.612939427691	-0.208215335902	0.217029938703	0.0290043163771	-0.0119917256435	0.258834776597	0.0351112060632	0.217396484798	22.1732211589	8.79463545103	-7.84606936634
16	3.22662449412	0.403418332573	0.00504208718623	1.22627727618	0.377301939753	6.07109346018	0.0930980395165	0.0261831231522	0.193426242448	-0.0982534864572	-0.00610726412761	-0.101807725981	-0.284798993176	0.265073330326	-0.114796048843	0.205252989093	0.0132091810409	0.0218190626712	0.192289729261	0.0170805786441	0.234060895323	16.5026541042	16.2303194935	-8.86556858601
17	3.0529393259	0.623922522501	0.458533511494	1.49477382629	-0.237672948642	6.91437666496	0.124516117243	-0.230799756785	0.223389280808	0.0531426364056	-0.0196648475542	0.0935360565371	-0.0598511904259	-0.172699797916	-0.12391626182	0.18364416163	0.0339037907742	0.00767561928119	0.191576859934	-0.00709468508207	0.228523606822	10.5901319869	14.4856912897	-5.22313390588

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 2 through 18 )	A	A	2 - 18	1 - 17
2	2	chain 'A' and (resid 19 through 34 )	A	A	19 - 34	18 - 33
3	3	chain 'A' and (resid 35 through 46 )	A	A	35 - 46	34 - 45
4	4	chain 'A' and (resid 47 through 61 )	A	A	47 - 61	46 - 60
5	5	chain 'A' and (resid 62 through 68 )	A	A	62 - 68	61 - 67
6	6	chain 'A' and (resid 69 through 84 )	A	A	69 - 84	68 - 83
7	7	chain 'A' and (resid 85 through 99 )	A	A	85 - 99	84 - 98
8	8	chain 'A' and (resid 100 through 109 )	A	A	100 - 109	99 - 108
9	9	chain 'A' and (resid 110 through 119 )	A	A	110 - 119	109 - 118
10	10	chain 'A' and (resid 120 through 129 )	A	A	120 - 128	119 - 127
11	11	chain 'B' and (resid 2 through 18 )	B	B	2 - 18	1 - 17
12	12	chain 'B' and (resid 19 through 45 )	B	B	19 - 45	18 - 44
13	13	chain 'B' and (resid 46 through 52 )	B	B	46 - 52	45 - 51
14	14	chain 'B' and (resid 53 through 65 )	B	B	53 - 65	52 - 64
15	15	chain 'B' and (resid 66 through 84 )	B	B	66 - 84	65 - 83
16	16	chain 'B' and (resid 85 through 109 )	B	B	85 - 109	84 - 108
17	17	chain 'B' and (resid 110 through 127 )	B	B	110 - 127	109 - 126

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