PDB-8gkj: Crystal Structure of the Murine MUC16 Specific Antibody AR9.6

ID or keywords:

Entry

Database: PDB / ID: 8gkj

Title

Crystal Structure of the Murine MUC16 Specific Antibody AR9.6

Components

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

Keywords

IMMUNE SYSTEM / antibody / Fab / CA125

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Brooks, C.L. / Aguilar, E.N.

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 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gk/8gkj ftp://data.pdbj.org/pub/pdb/validation_reports/gk/8gkj	HTTPS FTP

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Related structure data

Related structure data	8gkkC 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

A: MUC16 antibody AR9.6 heavy chain

B: MUC16 antibody AR9.6 light chain

C: MUC16 antibody AR9.6 heavy chain

D: MUC16 antibody AR9.6 light chain

98.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: MUC16 antibody AR9.6 heavy chain

B: MUC16 antibody AR9.6 light chain

defined by author&software
49.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: MUC16 antibody AR9.6 heavy chain

D: MUC16 antibody AR9.6 light chain

defined by author&software
49.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.302, 96.820, 105.449
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: 25216.111 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody	MUC16 antibody AR9.6 light chain Mass: 23884.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H₂O
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: 2.14 Å³/Da / Density % sol: 42.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 0.1M MES pH 5.7 6% tascimate pH 6.0 26% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 1, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 1.9→64.88 Å / Num. obs: 65609 / % possible obs: 97.75 % / Redundancy: 13.9 % / B_iso Wilson estimate: 28.51 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.1487 / R_pim(I) all: 0.041 / Net I/σ(I): 18.65
Reflection shell	Resolution: 1.9→1.968 Å / Num. unique obs: 6229 / CC_1/2: 0.834

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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: 1.9→64.88 Å / SU ML: 0.1827 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4669
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2189	3290	5.02 %
R_work	0.1821	62230	-
obs	0.184	65520	97.75 %

Solvent computation

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

Displacement parameters

B_iso mean: 33.24 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→64.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6533	0	0	577	7110

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0043	6706
X-RAY DIFFRACTION	f_angle_d	0.7763	9158
X-RAY DIFFRACTION	f_chiral_restr	0.0501	1030
X-RAY DIFFRACTION	f_plane_restr	0.0054	1173
X-RAY DIFFRACTION	f_dihedral_angle_d	5.7979	935

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 (%)
1.9-1.93	0.276	136	0.2543	2414	X-RAY DIFFRACTION	92.63
1.93-1.96	0.2806	133	0.2315	2476	X-RAY DIFFRACTION	94.7
1.96-1.99	0.2674	128	0.2126	2566	X-RAY DIFFRACTION	96.87
1.99-2.02	0.244	139	0.1954	2545	X-RAY DIFFRACTION	97.6
2.02-2.05	0.2357	139	0.2035	2542	X-RAY DIFFRACTION	97.28
2.05-2.09	0.2589	142	0.1893	2527	X-RAY DIFFRACTION	97.59
2.09-2.13	0.2146	116	0.1789	2582	X-RAY DIFFRACTION	97.75
2.13-2.17	0.2373	137	0.1873	2580	X-RAY DIFFRACTION	97.59
2.17-2.22	0.2591	129	0.1815	2559	X-RAY DIFFRACTION	97.39
2.22-2.27	0.2321	132	0.183	2595	X-RAY DIFFRACTION	98.06
2.27-2.33	0.2599	131	0.1794	2570	X-RAY DIFFRACTION	98.15
2.33-2.39	0.2087	134	0.1829	2600	X-RAY DIFFRACTION	98.17
2.39-2.46	0.2243	127	0.1849	2551	X-RAY DIFFRACTION	97.56
2.46-2.54	0.2482	136	0.1888	2617	X-RAY DIFFRACTION	98.46
2.54-2.63	0.2934	123	0.1969	2594	X-RAY DIFFRACTION	97.98
2.63-2.74	0.2285	167	0.1956	2577	X-RAY DIFFRACTION	98.28
2.74-2.86	0.2592	155	0.1881	2617	X-RAY DIFFRACTION	98.89
2.86-3.02	0.2209	131	0.1841	2638	X-RAY DIFFRACTION	99.14
3.02-3.2	0.1889	150	0.1823	2613	X-RAY DIFFRACTION	98.61
3.2-3.45	0.2189	141	0.1671	2628	X-RAY DIFFRACTION	98.79
3.45-3.8	0.1905	136	0.1668	2624	X-RAY DIFFRACTION	97.73
3.8-4.35	0.1873	128	0.1546	2712	X-RAY DIFFRACTION	99.3
4.35-5.48	0.1723	146	0.1568	2709	X-RAY DIFFRACTION	99.48
5.48-64.88	0.2357	154	0.2212	2794	X-RAY DIFFRACTION	98.01

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	1.29360626202	1.63488614081	0.25806545765	2.89580607464	1.32210321697	1.90728243985	-0.0199447472685	-0.0229912823776	-0.120854282957	0.0820357330547	0.130024717787	-0.338943515828	-0.0185023094666	0.19731306327	-0.136438400001	0.213774184084	0.0214715849626	0.0114962725689	0.323881558037	-0.0325148776679	0.25649346633	-31.3191859658	1.69590174475	25.7781486228
2	2.51815071885	1.53667103352	0.128641303711	5.24045248686	-0.132016376744	1.31033486767	-0.138873691192	0.130357190922	0.055711371009	-0.586799982513	0.0285672759655	0.190495041784	0.103585564996	-0.174599957213	0.103499809668	0.268214089664	-0.00576559625318	0.00367042191734	0.226887866835	0.00669259697182	0.188261268035	-23.3248892929	15.8058494025	-7.57624854707
3	1.32978378214	0.661289660981	-0.913027610917	1.37697441995	-0.615235921095	0.588928906889	-0.120917162504	-0.074992304055	-0.0408680154133	-0.170856205607	-0.00119193112567	0.0786804950849	0.0599896822314	0.0318124678843	0.117093925306	0.224144116729	0.0200192174287	-0.0403036793084	0.275252946781	-0.0143795761722	0.197690500176	-36.0474990253	7.08678894756	12.7180129889
4	4.58964905963	-3.94940440693	-4.32112284811	3.36480944918	3.77356829344	4.16987036113	0.703239455127	0.493374801972	0.50984663885	-0.546740863322	-0.33227940342	-0.0527839811366	-1.14556726748	-0.386935132313	-0.464769542917	0.316589963714	0.0324161357683	0.0298171104484	0.296126761397	0.059766938335	0.28836924821	-47.8390869776	3.96753869958	11.6806364975
5	3.482234324	1.39937102145	-2.75164996393	2.18701287555	0.278679354398	5.04372006141	0.28646560072	0.0633351605192	0.5744720059	-0.219640403392	0.161453141193	-0.0497410073342	-0.484518955642	0.185293442759	-0.483322441412	0.241076076619	0.016466149338	-0.0371686748267	0.192700244473	0.0287673263308	0.229088041312	-42.7342359501	5.48445903826	14.4726001112
6	2.76865694352	-0.383806909031	-3.54685649132	1.76589299117	1.11339766887	8.13948013123	-0.0584774358916	0.114372653606	-0.0462487023386	-0.0357808126034	-0.0142625503937	0.216966191514	0.203868796606	-0.328676642908	0.0761467085077	0.180661533958	0.0284823352305	-0.0313991906204	0.212380130147	0.00977430277036	0.279323134984	-50.2970955244	1.17892871097	22.0171369071
7	6.87176697491	-2.63547425874	5.2768498764	1.00142218738	-1.69313780765	4.91355802852	-0.0628114848184	-0.0615397090348	-0.106649851445	0.0863543178159	0.0837812829308	0.165616624564	-0.0756918003438	-0.17126150624	-0.0695747244361	0.210935411388	-0.0125516091981	0.046061092498	0.242999278827	0.0211905256211	0.249748319075	-29.0052511296	-22.4772299778	14.9125465864
8	8.99909789564	3.45142558849	-0.735924538452	6.74504374987	-0.293000997669	5.52407071821	0.0268984938493	0.0454372830395	-0.450003805617	-0.145781865378	-0.0841512488376	-0.167257900057	0.215197392369	0.312038823737	0.038170738947	0.219770743264	0.0526798873559	0.0156522450334	0.147040653279	-0.00161054733057	0.138799017519	-22.710621571	-26.7540131632	7.37425242236
9	6.42056211033	0.853340515921	1.53376546749	2.83927012143	-0.939811595072	4.69286154208	-0.097561404492	-0.212473347385	-0.228102741218	0.188328133659	-0.0823141655422	-0.134141800415	0.350190448784	0.35305854469	0.183618863342	0.294884846928	-0.0194008154078	0.0170049772611	0.203871796538	0.0432456753333	0.269135390168	-27.4044598196	-32.7683305567	11.4641197217
10	1.16943241227	0.473315622493	1.2120491883	0.473528766973	0.154402857862	3.73350386503	-0.00610448057919	-0.0719765622328	-0.0796024480534	-0.00377969217909	-0.0364630866678	-0.0394804508411	0.140959904965	-0.0167348058286	0.0324339086851	0.216652913001	0.0173674418721	0.020420083126	0.225381584455	0.0196233257048	0.268492934469	-22.4216920101	-22.9307220557	11.7881786985
11	5.64542707165	-1.1751128164	3.33092397558	0.902865230936	0.41788510747	3.87173047334	-0.364903977587	0.160977010024	0.670877556368	-0.629557108919	-0.160801430987	-0.415789577775	-0.175986274087	0.439199056057	0.439410186871	0.232240666624	0.037345372538	-0.019564571714	0.274911545854	-0.0171778353663	0.316884989026	1.74945824864	6.78840576329	26.6073610946
12	2.56892577908	2.65905315586	0.389854010305	6.43433951919	-0.551580125477	1.49926773111	-0.052755067311	0.0215474910817	0.280492931437	-0.0644845831679	-0.00396444569666	0.218866737605	-0.0172419672765	-0.0960562085778	0.0605238407599	0.137914007783	0.0155912302256	-0.00028410571925	0.219086651369	0.00960975581251	0.195994708364	-8.01724024869	-0.87622532756	23.7149640486
13	7.5018160422	7.04675558912	-1.61598429195	9.00584670523	-1.8174266857	2.39043856601	-0.0805134610785	-0.318253475338	0.446975084832	0.243245053864	0.139562808972	0.184275898447	0.290471582491	-0.148667423824	-0.0528856876874	0.2992410871	0.0293729828511	0.0235016774192	0.37370554609	-0.0840710698027	0.370866226876	-7.78051409862	2.42037718005	32.7000176226
14	2.02661523033	0.8445880022	-0.696579522482	3.26730818209	-0.500919801547	1.0309577712	-0.105763068192	0.0986658292893	-0.0205436585835	-0.207034232215	0.0947662546175	-0.118002387937	0.0470714583593	0.113028315614	0.015396484249	0.24387574531	0.000858369139397	0.0185378450344	0.237217553695	-0.00918707811202	0.210799622498	-15.524768263	-16.4100000298	-7.08524415001
15	5.22800518402	6.64727917184	1.84239828355	6.95698690344	1.99053106545	0.43193234253	-0.299863320565	0.318969431254	0.00901517758872	-0.65252073249	0.249013041042	-0.185614761518	0.0682247494287	0.178022842024	-0.0739581119695	0.344017865892	0.0264484679063	0.0982684213939	0.26576323319	-0.0134501928643	0.332993096413	-9.87667605869	-15.2516595726	-0.974238837709
16	2.47958794166	-1.13536270558	3.33162851766	0.989003482227	-1.57364309759	8.73837416263	0.031868786201	-0.0152621104946	0.12329974597	0.00686859295512	0.00472610115705	-0.030539075068	0.0145143245891	-0.391505959302	-0.0442112065643	0.157370439875	-0.0234696281117	0.0102256363705	0.171421095214	0.0083169061522	0.245074714727	5.47304226637	-1.38944971069	20.5599684777
17	3.74027860975	-0.152919962161	3.79494066411	1.10832845872	-0.795186106709	6.84840958831	0.00169170073777	-0.0269917214306	0.176182120597	-0.0684359380601	-0.00501330340948	-0.0211396169992	-0.0407171718633	0.0923794931295	0.020476611813	0.184205141949	0.0291661973625	0.0377073424012	0.197508725792	-0.0213027433621	0.286190373629	8.87515379781	-1.8641879773	19.5643313172
18	1.71457368068	0.581834227506	-0.357349320186	2.88320447395	0.211188437187	3.11730666061	0.000747833630805	-0.0201849849614	0.0474340517097	0.0886474730576	-0.111058744478	-0.352283830346	-0.0475752271361	-0.022953922335	0.113540855619	0.159076075055	-0.00845918948716	-0.0305911002867	0.181932748341	0.0189486567144	0.272609065806	-13.4863828909	25.0457633907	9.90098400193

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 'C' and (resid 122 through 222 )	C	C	122 - 222	122 - 218
2	2	chain 'D' and (resid 1 through 94 )	D	D	1 - 94	1 - 94
3	3	chain 'D' and (resid 95 through 143 )	D	D	95 - 143	95 - 143
4	4	chain 'D' and (resid 144 through 154 )	D	D	144 - 154	144 - 154
5	5	chain 'D' and (resid 155 through 176 )	D	D	155 - 176	155 - 176
6	6	chain 'D' and (resid 177 through 217 )	D	D	177 - 217	177 - 217
7	7	chain 'A' and (resid 2 through 33 )	A	A	2 - 33	1 - 32
8	8	chain 'A' and (resid 34 through 57 )	A	A	34 - 57	33 - 56
9	9	chain 'A' and (resid 58 through 76 )	A	A	58 - 76	57 - 75
10	10	chain 'A' and (resid 77 through 129 )	A	A	77 - 129	76 - 128
11	11	chain 'A' and (resid 130 through 144 )	A	A	130 - 144	129 - 143
12	12	chain 'A' and (resid 145 through 212 )	A	A	145 - 212	144 - 211
13	13	chain 'A' and (resid 213 through 224 )	A	A	213 - 224	212 - 223
14	14	chain 'B' and (resid 1 through 94 )	B	B	1 - 94	1 - 94
15	15	chain 'B' and (resid 95 through 117 )	B	B	95 - 117	95 - 117
16	16	chain 'B' and (resid 118 through 154 )	B	B	118 - 154	118 - 154
17	17	chain 'B' and (resid 155 through 218 )	B	B	155 - 218	155 - 218
18	18	chain 'C' and (resid 1 through 121 )	C	C	1 - 121	1 - 121

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Open data

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Download

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Validation report

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Assembly

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Yorodumi