PDB-8gkk: Crystal Structure of the Humanized MUC16 Specific Antibody huAR9.6

ID or keywords:

Entry

Database: PDB / ID: 8gkk

Title

Crystal Structure of the Humanized MUC16 Specific Antibody huAR9.6

Components

MUC16 antibody AR9.6 heavy chain
MUC16 antibody AR9.6 light chain

Keywords

IMMUNE SYSTEM / Fab / CA125

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Brooks, C.L. / Murray, B.

Funding support

United States, 1items

Citation

Journal: Mol.Cancer Ther. / Year: 2024
Title: Structural Basis for Multivalent MUC16 Recognition and Robust Anti-Pancreatic Cancer Activity of Humanized Antibody AR9.6.
Authors: Aguilar, E.N. / Sagar, S. / Murray, B.R. / Rajesh, C. / Lei, E.K. / Michaud, S.A. / Goodlett, D.R. / Caffrey, T.C. / Grandgenett, P.M. / Swanson, B. / Brooks, T.M. / Black, A.R. / van ...

History

Deposition	Mar 19, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 20, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 2, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8gkk.cif.gz	311.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8gkk.ent.gz	210.2 KB	Display	PDB format
PDBx/mmJSON format	8gkk.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/gk/8gkk ftp://data.pdbj.org/pub/pdb/validation_reports/gk/8gkk	HTTPS FTP

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Related structure data

Related structure data	8gkjC 8gklC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

H: MUC16 antibody AR9.6 heavy chain

L: MUC16 antibody AR9.6 light chain

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	66.736, 94.974, 110.565
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
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

#1: Antibody	MUC16 antibody AR9.6 heavy chain Mass: 23988.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	MUC16 antibody AR9.6 light chain Mass: 23654.174 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 692 / 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: 3.68 Å³/Da / Density % sol: 66.55 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris, pH 7.0 2.2 M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9793 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.75→57.14 Å / Num. obs: 436695 / % possible obs: 97.57 % / Redundancy: 6.3 % / B_iso Wilson estimate: 22.27 Å² / CC_1/2: 0.905 / R_merge(I) obs: 0.07045 / R_pim(I) all: 0.03076 / Net I/σ(I): 14.07
Reflection shell	Resolution: 1.75→1.813 Å / R_merge(I) obs: 0.5148 / Num. unique obs: 33472 / CC_1/2: 0.785 / R_pim(I) all: 0.23577

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
xia2		data reduction
xia2		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75→57.14 Å / SU ML: 0.1844 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 17.3743
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1915	3514	5.03 %
R_work	0.1671	66284	-
obs	0.1683	69798	97.57 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 26.14 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→57.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3249	0	5	692	3946

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0062	3338
X-RAY DIFFRACTION	f_angle_d	0.8665	4554
X-RAY DIFFRACTION	f_chiral_restr	0.0569	513
X-RAY DIFFRACTION	f_plane_restr	0.0055	585
X-RAY DIFFRACTION	f_dihedral_angle_d	6.1549	467

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 (%)
1.75-1.77	0.2759	115	0.2722	2139	X-RAY DIFFRACTION	80.5
1.77-1.8	0.277	127	0.2499	2527	X-RAY DIFFRACTION	92.54
1.8-1.83	0.2612	138	0.2425	2502	X-RAY DIFFRACTION	95.1
1.83-1.85	0.2446	152	0.2292	2593	X-RAY DIFFRACTION	97.1
1.85-1.89	0.2351	112	0.2008	2646	X-RAY DIFFRACTION	97.46
1.89-1.92	0.2146	137	0.1877	2644	X-RAY DIFFRACTION	97.89
1.92-1.95	0.2101	151	0.1847	2636	X-RAY DIFFRACTION	98.17
1.95-1.99	0.2233	143	0.1683	2620	X-RAY DIFFRACTION	98.15
1.99-2.03	0.2093	139	0.1686	2665	X-RAY DIFFRACTION	98.18
2.03-2.07	0.2153	125	0.1759	2655	X-RAY DIFFRACTION	98.3
2.07-2.12	0.1989	150	0.1763	2626	X-RAY DIFFRACTION	98.4
2.12-2.18	0.2081	144	0.1767	2648	X-RAY DIFFRACTION	98.59
2.18-2.24	0.1585	131	0.158	2688	X-RAY DIFFRACTION	98.64
2.24-2.3	0.1837	137	0.1478	2671	X-RAY DIFFRACTION	98.53
2.3-2.38	0.1969	150	0.1504	2656	X-RAY DIFFRACTION	98.39
2.38-2.46	0.1783	150	0.1508	2673	X-RAY DIFFRACTION	99.12
2.46-2.56	0.1962	148	0.1545	2670	X-RAY DIFFRACTION	98.98
2.56-2.67	0.1864	147	0.1593	2697	X-RAY DIFFRACTION	99.06
2.68-2.82	0.2044	140	0.1677	2692	X-RAY DIFFRACTION	99.02
2.82-2.99	0.2216	131	0.1655	2706	X-RAY DIFFRACTION	98.95
2.99-3.22	0.1867	168	0.1568	2710	X-RAY DIFFRACTION	99.45
3.22-3.55	0.1516	156	0.1474	2727	X-RAY DIFFRACTION	99.41
3.55-4.06	0.169	141	0.1451	2748	X-RAY DIFFRACTION	99.62
4.06-5.12	0.1526	150	0.1356	2799	X-RAY DIFFRACTION	99.8
5.12-10	0.2342	132	0.2253	2946	X-RAY DIFFRACTION	99.55

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	5.57624648573	1.609440241	-4.29779920587	1.24214031629	-1.52997076047	3.41883716485	-0.222857002519	-0.0806333678306	-0.205989125486	0.00862266508489	-0.115808385225	-0.148776981003	-0.188546715359	0.22043062061	0.376943225942	0.214571934409	0.0159003553583	-0.0501766673384	0.234256163553	0.0377814944875	0.222011045707	27.7152495843	51.2678675571	39.7517977251
2	1.68361708069	0.68436982265	-0.317396434101	1.4679131501	-0.712123762835	1.66413441718	0.0387345933264	-0.0602341413772	0.0919551150977	0.130823915379	0.00998068349754	0.0754961757128	-0.13093178833	-0.0331359401763	-0.0500874990049	0.185787609134	0.00239063282757	0.0194219192196	0.17868269036	0.0161131065735	0.157122451776	24.0011605253	55.4577589037	29.2824639338
3	7.46379443766	1.85650599071	-0.0269463722007	3.40045120041	0.241057018982	3.63463008644	-0.1503012285	-0.660302263136	0.0206441592128	0.263130939321	0.0103448412266	0.300428742629	-0.309762042368	-0.300929972005	0.120567534356	0.241349867175	0.0403378565112	0.02730828552	0.185776967193	0.0259886487395	0.152952057888	21.8361495815	61.1222913493	33.6635734257
4	0.716789659225	-0.0752194103076	-2.13865712039	4.90905325106	-0.943098855097	6.64481872124	0.0830973531045	-0.0309892422755	0.148765889459	0.33810774911	0.0161596450888	0.407958229692	-0.466276770563	-0.216892410959	-0.160501430371	0.188026829839	0.038633519603	-0.0291424454011	0.191424915116	0.00470261299673	0.152388185602	21.0399439293	56.332519764	39.9662710625
5	1.1400153036	0.400533710232	-1.56008223479	0.636105152235	-0.966288793533	6.71212085069	-0.055096398513	-0.0562021383103	0.0241238017382	-0.0700266277139	0.0231329244689	-0.0588866553786	0.0340634978914	0.12325395404	0.0524913723573	0.195514515324	-0.0159979606144	-0.00132658136469	0.150863869548	0.0161467301609	0.186799764163	25.0398706146	49.8395363105	24.8290394336
6	0.509012522538	-0.839085919678	-0.402732305278	3.89204602384	0.866874241004	1.31671616843	-0.0514134608142	-0.02490042948	-0.0533443905847	0.0699341684117	0.0703633767526	0.0523904795786	-0.00679029232981	0.0195678716625	-0.0201840603196	0.0984401327992	-0.000694971993858	-0.000254290370274	0.172013417997	-0.00971657818572	0.146969612303	27.7018425237	28.6343811834	47.9012690789
7	1.65400768887	-2.66603816684	-0.294549332799	9.84563046895	0.696176782156	0.807872181475	-0.0187950838506	0.0651718464449	0.127426947285	0.262097486707	0.056385293348	-0.607674264995	0.0220696733598	0.0491061744543	-0.033304213178	0.108564185119	0.00294297472075	-0.0293676731176	0.173190253176	-0.0247981540781	0.174007013751	36.9334394518	27.3824141236	49.9914621252
8	3.76961519393	-3.33840774908	0.271236892703	6.02551170204	-1.01192711121	1.40385514982	0.0596049939454	0.0316558734913	-0.346231910649	-0.344139250544	0.153767843681	0.526500530237	0.281388033264	-0.222731442622	-0.196707070051	0.253898064607	-0.0531151788127	-0.0394374672007	0.256510652594	0.0592097015043	0.243412509505	9.13648827613	34.9528762046	20.6004430212
9	2.30892889016	-0.945128828659	1.01135084545	3.3161750506	-1.18409022271	3.1875765274	-0.000332587537188	0.0887945741276	-0.0697439235302	-0.196156054651	0.01233726136	0.017045332549	0.0515676684839	-0.0276989168134	-0.00258252335394	0.165078664379	-0.0253192791327	0.00205173842024	0.159706594313	0.0246355263023	0.150551543715	16.2327641987	42.896525345	15.9029235856
10	0.252276933115	-0.292696373815	0.210258587384	1.80934056777	-1.48308419896	1.29037891751	-0.0201499385084	0.000749275853371	0.000685052906499	-0.121303517997	0.0900158184425	0.0582979047171	0.0514020782777	-0.0940921635643	-0.0682137279745	0.14918857138	-0.00124933815557	0.00418030136886	0.197429265815	0.0058968640349	0.183702228057	18.2759285119	30.8581201274	32.2789566919
11	2.06738448805	0.420131116832	-1.21611486368	0.631251277725	-0.0699602018769	5.19770353683	-0.0346486564438	0.014250001928	-0.0540107450447	-0.0783340080421	0.0557658561548	0.186852683944	-0.0529445874806	-0.271739929142	0.0241597449544	0.152197299505	0.0274822601839	-0.00126204895523	0.141935702004	0.0110032423478	0.194459634072	16.4477457701	18.1569652765	44.7920776732
12	1.96959619678	2.26471732187	-3.21509679584	4.66994440123	-5.19268565694	7.1945325963	0.0125679565865	-0.0349590340587	-0.0547124331021	-0.116089019796	0.070715783873	0.254167810785	0.205498929566	-0.203928552094	-0.0877893584207	0.130425968373	0.00279487486876	0.00674174125232	0.202831715928	0.00291347988981	0.210687132581	11.5236794223	19.6516926707	52.555021744
13	0.840175251791	0.538277453146	-1.35729518809	1.10014726072	-1.35552234419	9.40715460646	0.056518698526	-0.168916433999	-0.0360327252046	0.0859370547884	0.0257333057509	0.0508201497523	-0.120585977663	0.187277778333	-0.0613160227953	0.135411894914	0.021885854241	0.00197141829166	0.185613481579	0.0150341356378	0.192717097522	19.8249359912	21.8352756106	46.4415898286
14	1.93163200164	0.674131362234	1.3634241718	1.81376603182	0.274827572661	8.71573288567	-0.0242383168193	-0.0677056169908	-0.194983205162	0.0180758462379	0.00385100092522	0.0821074667064	0.551109087264	-0.284525804086	-0.0145852054438	0.183708585066	-0.000127471601329	0.0270414846014	0.185639955464	0.0255176755026	0.248338824036	15.9498107049	10.2375979708	49.1167254432

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 'H' and (resid 1 through 17 )	H	A	1 - 17	1 - 17
2	2	chain 'H' and (resid 18 through 60 )	H	A	18 - 60	18 - 60
3	3	chain 'H' and (resid 61 through 76 )	H	A	61 - 76	61 - 76
4	4	chain 'H' and (resid 77 through 91 )	H	A	77 - 91	77 - 91
5	5	chain 'H' and (resid 92 through 119 )	H	A	92 - 119	92 - 119
6	6	chain 'H' and (resid 120 through 198 )	H	A	120 - 198	120 - 193
7	7	chain 'H' and (resid 199 through 224 )	H	A	199 - 224	194 - 219
8	8	chain 'L' and (resid 1 through 24 )	L	C	1 - 24	1 - 24
9	9	chain 'L' and (resid 25 through 79 )	L	C	25 - 79	25 - 79
10	10	chain 'L' and (resid 80 through 132 )	L	C	80 - 132	80 - 132
11	11	chain 'L' and (resid 133 through 154 )	L	C	133 - 154	133 - 154
12	12	chain 'L' and (resid 155 through 167 )	L	C	155 - 167	155 - 167
13	13	chain 'L' and (resid 168 through 192 )	L	C	168 - 192	168 - 192
14	14	chain 'L' and (resid 193 through 215 )	L	C	193 - 215	193 - 215

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