PDB-8jyq: Crystal structure of cancer-specific anti-HER2 antibody H2Mab-214...

ID or keywords:

Entry

Database: PDB / ID: 8jyq

Title

Crystal structure of cancer-specific anti-HER2 antibody H2Mab-214 in complex with epitope peptide

Components

H2CasMab-1 VH(S112C),SARAH
H2CasMab-1 VL,SARAH(S37C)
H2CasMab-1 epitope peptide

Keywords

IMMUNE SYSTEM / HER2 / antibody

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Arimori, T. / Takagi, J.

Funding support

Japan, 2items

Citation

Journal: Structure / Year: 2024
Title: Locally misfolded HER2 expressed on cancer cells is a promising target for development of cancer-specific antibodies.
Authors: Arimori, T. / Mihara, E. / Suzuki, H. / Ohishi, T. / Tanaka, T. / Kaneko, M.K. / Takagi, J. / Kato, Y.

History

Deposition	Jul 3, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 13, 2024	Provider: repository / Type: Initial release
Revision 1.1	Mar 27, 2024	Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	May 15, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8jyq.cif.gz	344.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8jyq.ent.gz	233.9 KB	Display	PDB format
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Validation report

Summary document	8jyq_validation.pdf.gz	468.1 KB	Display	wwPDB validaton report
Full document	8jyq_full_validation.pdf.gz	475.4 KB	Display
Data in XML	8jyq_validation.xml.gz	26.6 KB	Display
Data in CIF	8jyq_validation.cif.gz	37.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jy/8jyq ftp://data.pdbj.org/pub/pdb/validation_reports/jy/8jyq	HTTPS FTP

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Related structure data

Related structure data	8jyrC 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: H2CasMab-1 VH(S112C),SARAH

B: H2CasMab-1 VL,SARAH(S37C)

C: H2CasMab-1 epitope peptide

D: H2CasMab-1 VH(S112C),SARAH

E: H2CasMab-1 VL,SARAH(S37C)

F: H2CasMab-1 epitope peptide

79.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: H2CasMab-1 VH(S112C),SARAH

B: H2CasMab-1 VL,SARAH(S37C)

C: H2CasMab-1 epitope peptide

defined by author&software
39.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: H2CasMab-1 VH(S112C),SARAH

E: H2CasMab-1 VL,SARAH(S37C)

F: H2CasMab-1 epitope peptide

defined by author&software
39.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.143, 62.793, 78.122
Angle α, β, γ (deg.)	90.000, 94.419, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Antibody	H2CasMab-1 VH(S112C),SARAH Mass: 19726.330 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Production host: Homo sapiens (human)
#2: Antibody	H2CasMab-1 VL,SARAH(S37C) Mass: 18974.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human) Production host: Homo sapiens (human)
#3: Protein/peptide	H2CasMab-1 epitope peptide Mass: 1034.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.35 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES pH 9.5, 20% w/v PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 2, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 1.75→47.58 Å / Num. obs: 70833 / % possible obs: 98.6 % / Redundancy: 3.86 % / B_iso Wilson estimate: 36.08 Å² / CC_1/2: 0.998 / R_sym value: 0.052 / Net I/σ(I): 10.95
Reflection shell	Resolution: 1.75→1.85 Å / Redundancy: 3.83 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 11237 / CC_1/2: 0.708 / R_sym value: 0.961 / % possible all: 97.2

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75→36.46 Å / SU ML: 0.2859 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1081
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2334	3540	5 %
R_work	0.1958	67233	-
obs	0.1977	70773	98.5 %

Solvent computation

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

Displacement parameters

B_iso mean: 53.94 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→36.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5355	0	0	193	5548

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5519
X-RAY DIFFRACTION	f_angle_d	0.8811	7479
X-RAY DIFFRACTION	f_chiral_restr	0.0561	827
X-RAY DIFFRACTION	f_plane_restr	0.0074	952
X-RAY DIFFRACTION	f_dihedral_angle_d	5.7049	739

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	0.5228	132	0.4946	2488	X-RAY DIFFRACTION	93.14
1.77-1.79	0.4682	140	0.4402	2669	X-RAY DIFFRACTION	97.77
1.79-1.82	0.4001	143	0.3899	2701	X-RAY DIFFRACTION	98.34
1.82-1.85	0.3772	140	0.3544	2664	X-RAY DIFFRACTION	98.52
1.85-1.88	0.4073	138	0.3198	2628	X-RAY DIFFRACTION	97.91
1.88-1.91	0.3256	142	0.2882	2700	X-RAY DIFFRACTION	99.09
1.91-1.95	0.3006	140	0.2877	2647	X-RAY DIFFRACTION	98.45
1.95-1.99	0.3084	141	0.2713	2682	X-RAY DIFFRACTION	98.47
1.99-2.03	0.3283	143	0.2689	2726	X-RAY DIFFRACTION	98.93
2.03-2.07	0.2943	140	0.2625	2664	X-RAY DIFFRACTION	99.12
2.07-2.12	0.2716	141	0.2266	2680	X-RAY DIFFRACTION	98.95
2.12-2.17	0.2512	143	0.2183	2727	X-RAY DIFFRACTION	98.9
2.17-2.23	0.2682	142	0.2196	2692	X-RAY DIFFRACTION	98.99
2.23-2.3	0.2573	141	0.2198	2677	X-RAY DIFFRACTION	98.88
2.3-2.37	0.2598	142	0.2248	2699	X-RAY DIFFRACTION	98.92
2.37-2.45	0.2717	143	0.2216	2717	X-RAY DIFFRACTION	99.06
2.45-2.55	0.2672	141	0.2242	2677	X-RAY DIFFRACTION	98.81
2.55-2.67	0.2878	142	0.2175	2682	X-RAY DIFFRACTION	98.53
2.67-2.81	0.2452	142	0.2176	2709	X-RAY DIFFRACTION	99.03
2.81-2.98	0.269	143	0.2134	2713	X-RAY DIFFRACTION	98.93
2.98-3.21	0.2288	143	0.2092	2720	X-RAY DIFFRACTION	98.96
3.22-3.54	0.2291	143	0.1871	2726	X-RAY DIFFRACTION	99.14
3.54-4.05	0.1982	144	0.1625	2719	X-RAY DIFFRACTION	98.83
4.05-5.1	0.1807	143	0.1382	2725	X-RAY DIFFRACTION	98.08
5.1-36.46	0.1785	148	0.1568	2801	X-RAY DIFFRACTION	98.83

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	6.52775155019	-1.77028572898	-0.646397205518	8.15201925662	-1.14500305818	3.59613114358	0.326684054472	0.505113544495	0.776015228969	-0.219238595661	-0.100373839334	-0.100906695832	-0.487062714238	0.0751848138783	-0.0155604235893	0.332311425361	-0.0354591273277	0.0955336842015	0.318262601796	0.0223145137355	0.325435646777	4.028	4.157	-11.813
2	1.93034136493	-2.48419916276	2.80759865662	3.59621384813	-4.05429657845	4.84970534688	-0.158683022094	-0.277131870731	-0.0682170416386	1.29417920442	0.157000456776	-0.007168358971	-0.668877238088	-0.0849754293546	0.0825766081115	0.458578096264	-0.0941455553099	0.0492589298569	0.436993542389	-0.0415040598513	0.323769145175	6.981	-3.512	-0.308
3	5.31970362745	1.79894763086	-1.81640695767	2.68648902471	-1.88425068512	7.94447830755	0.17818601495	-0.131252381599	0.0793589258101	1.05944519557	0.046004554602	0.240661395124	-0.31538044837	-0.139899324238	-0.250251196441	0.291425869856	0.0210698176705	0.0303644512391	0.31742100895	-0.0225766964291	0.316694779053	-0.628	0.029	-1.424
4	7.22323858317	0.882850719658	0.242726417199	2.25664391201	1.32536114325	4.82142983996	-0.0281929440167	-0.188309834361	-0.266198108075	0.644539597763	0.513579747649	0.385558177387	0.476077439706	-0.346579539311	-0.245402604201	0.342960745971	-0.045342404883	0.0291425343613	0.348625341048	0.0116930578336	0.288483293428	-5.432	0.882	-4.091
5	5.71655117904	-4.16484418931	0.480850677873	4.86416426064	-0.910210540024	1.32153774379	0.178005351581	0.101859536417	0.0778068420264	0.0485335534638	-0.113482142618	0.0516603228171	-0.152852064031	0.0292653176555	-0.055701786907	0.328451055919	-0.0451829916136	0.0331795999251	0.297009883724	-0.00819588389953	0.211896865787	4.762	-1.025	-13.011
6	4.15286643021	-5.6582943484	-0.344586583855	8.10835934197	1.05151982395	5.30121062484	0.537676134319	0.41809399233	0.331286496999	-0.599073903082	-0.456661350404	0.0436875022186	-0.106416511826	-0.22192684553	-0.144187319237	0.346691365128	-0.0649370283765	-0.000677276308695	0.308584505703	-0.0103385234517	0.304269793081	-3.225	1.558	-15.826
7	6.21448919757	1.80447199846	1.94480002707	7.17417466644	-2.36897683187	2.14501771977	0.00661282688742	-0.610238334501	1.05984424146	1.24707049012	-0.422949785203	0.495161851741	-0.653050152195	0.405207298381	0.348379249387	0.779726623849	0.0847865919293	0.0742208021881	0.718438345978	-0.188427028266	1.1365772925	-27.107	22.796	-9.791
8	9.09852541668	-6.42658950509	-9.29797939793	6.25971004661	6.8075276629	8.62073346237	0.887707595434	1.42103348136	0.0288223053068	-1.02571593815	-0.984899086172	0.424255006271	-0.869588498237	-1.33681172587	0.084230053828	0.584112838184	0.134957452557	-0.157877856124	0.618942842968	0.0605759008117	0.523789524342	-19.08	7.28	-31.902
9	2.59997390599	0.0159733129144	0.17756521648	3.22256774286	0.486619309012	8.79829843041	0.0390150804662	0.309506887366	0.109096654248	-0.30111202666	-0.325165265078	0.0231498868037	-0.0518813599985	0.0650056555761	0.319703822256	0.280403099339	-0.00209753842363	0.0541346244666	0.382243438752	0.0266312149971	0.284733295572	14.039	2.592	-25.4
10	3.64589887375	-0.951264937577	-1.41383122211	2.54979765912	2.10389052708	3.41248479192	0.0732964939438	-0.000442826075427	-0.05594757267	-0.110213360588	0.242438401786	-0.22912197996	0.281277880735	0.38063735689	-0.171283695171	0.472792102151	0.0522699447138	0.00460564701873	0.382453821044	0.0650818788247	0.419828892315	-13.871	3.147	-26.211
11	4.85102522393	-3.39686274731	-4.13107231883	2.82552348159	2.5989693199	3.69885552635	-0.1533525736	-0.941000889363	0.551098195524	0.923566780232	0.361023932719	-0.410586126903	0.310462005989	1.21874049468	-0.345742164164	0.470613669318	-0.0506075740022	-0.00719235846065	0.644360016506	-0.0118580365617	0.313006069769	17.12	-7.332	-4.837
12	1.60236194527	-0.0456242727578	0.51468432519	1.94944111003	-0.486037067522	3.69164597844	0.109426769481	0.127408160313	0.143549767136	-0.394362609437	-0.0119460627461	-0.0441830857241	-0.283962900197	0.189285959154	-0.0781203857966	0.467336115771	-0.0619984334444	0.0400154321363	0.294155533762	-0.00397019111749	0.326744667849	-31.574	-6.383	-20.444
13	4.86951427579	0.126123369062	0.410030193052	0.117746315899	0.810130881459	5.16401732654	-0.0805957342485	1.45557206283	-0.0741286021224	-0.00811473686119	0.0478037820766	-0.614946030716	0.640267823573	-0.300576972499	-0.1390316537	0.85191994912	-0.0464184368725	0.0226392339114	0.964980835416	-0.00867133830059	0.654208423375	-43.627	-7.563	-48.857
14	4.32128346157	0.759555631692	-1.31404095001	3.54872936155	-3.26314411762	7.26882611921	-0.108408192016	0.694890138928	-0.422983022675	-0.698546938797	0.691757217139	0.420857542899	1.07429363934	-1.23957247458	-0.118877306159	0.540168708264	-0.116027048889	0.00462272274348	0.696756132521	-0.112128054118	0.584177900206	-59.433	-18.682	-32.46
15	2.07419742196	1.43727488416	0.0982895115443	2.03250423024	1.84062570605	6.63627836055	-0.0415818986138	0.077838363967	-0.559727320906	-0.878626580939	0.0375460409291	-0.774656988902	-0.295229535155	0.70176172185	-0.0158064063643	0.466508184537	0.029521083355	0.145112016155	0.371911934499	0.010054014022	0.540019239129	-23.556	-25.358	-18.945
16	2.56011705057	0.469414786388	-1.66554726495	3.70533945804	0.402151077189	3.49780225096	0.0278575160927	-0.294682431206	-0.218436090342	0.154505369178	-0.0807869536868	-0.103584882239	0.0582011485179	0.321440263161	0.0369152430821	0.228769988199	0.00299201094514	-0.0263744529177	0.238444809869	0.0477194672458	0.285369960438	-32.948	-24.071	-8.424
17	5.79084983131	1.02220252398	-0.123708898642	1.92474471286	2.78048832121	6.62644586217	-0.277248230968	0.378333675455	-1.62123199603	0.674974172636	0.00385075190246	0.332375571847	0.972139584671	-1.79815000569	0.230435252977	0.563556904473	-0.107575268939	0.0454625618548	0.706670541004	0.0578331253806	0.768359535751	-48.671	-31.14	-11.309
18	2.41670469165	2.26496067238	-2.73688466948	7.59027245374	-6.46973811997	4.9896577085	-0.467445631399	0.0539143298528	-0.418169732879	0.434785567126	-0.0632614610527	-0.658844329372	-0.796958786059	-0.383731987218	0.523745477128	0.487324583074	0.0489070090072	0.0146377112543	0.585488513064	-0.141692788459	0.597912096864	-52.196	-13.982	-28.133
19	5.52275009859	-0.039910589478	0.996833062388	2.08790209334	-0.463565330057	7.56863747244	0.300660171428	-0.404718237506	-0.221747243736	-0.122534954485	-0.19947752239	-0.805294578653	-0.0767655973218	1.3776667386	0.304392152485	0.418890684154	-0.101885662508	-0.0331613588893	0.54767926855	-0.0152566126325	0.51276991328	-17.472	-8.274	-6.888
20	4.8964548842	0.432084504136	-4.60060977654	2.84904201777	0.773214498372	4.86621280467	0.41035506526	1.1097416211	-0.440492714989	-0.841963872718	-0.703601826806	1.25858509598	0.160264178398	-0.979127946778	0.474931654204	0.49747864858	-0.00712672811563	-0.0095342795191	0.430607906828	-0.0604929806719	0.460710789111	-4.269	-9.298	-15.644
21	3.96972866644	-2.85005347263	-0.630477863973	6.24306276228	-0.275794346187	0.989223273102	0.008204124346	0.0317992126241	-0.0810798260018	0.134880833954	0.00335009446941	0.204915505611	0.0927405382238	-0.0708720763324	-0.0036470741118	0.382938958145	-0.0333450586216	0.00547757066345	0.38703795478	-0.0103442306065	0.275631530824	-3.768	-1.833	-8.589

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN D AND RESID 40:52 )	D	40 - 52
2	X-RAY DIFFRACTION	2	( CHAIN D AND RESID 53:60 )	D	53 - 60
3	X-RAY DIFFRACTION	3	( CHAIN D AND RESID 61:75 )	D	61 - 75
4	X-RAY DIFFRACTION	4	( CHAIN D AND RESID 76:82 )	D	76 - 82
5	X-RAY DIFFRACTION	5	( CHAIN D AND RESID 83:100 )	D	83 - 100
6	X-RAY DIFFRACTION	6	( CHAIN D AND RESID 101:113 )	D	101 - 113
7	X-RAY DIFFRACTION	7	( CHAIN D AND RESID 114:124 )	D	114 - 124
8	X-RAY DIFFRACTION	8	( CHAIN D AND RESID 125:163 )	D	125 - 163
9	X-RAY DIFFRACTION	9	( CHAIN E AND RESID 0:112 )	E	0 - 112
10	X-RAY DIFFRACTION	10	( CHAIN E AND RESID 113:162 )	E	113 - 162
11	X-RAY DIFFRACTION	11	( CHAIN F AND RESID 612:618 )	F	612 - 618
12	X-RAY DIFFRACTION	12	( CHAIN A AND RESID 1:109 )	A	1 - 109
13	X-RAY DIFFRACTION	13	( CHAIN A AND RESID 110:124 )	A	110 - 124
14	X-RAY DIFFRACTION	14	( CHAIN A AND RESID 125:161 )	A	125 - 161
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 0:7 )	B	0 - 7
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 8:101 )	B	8 - 101
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 102:119 )	B	102 - 119
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 120:159 )	B	120 - 159
19	X-RAY DIFFRACTION	19	( CHAIN C AND RESID 611:618 )	C	611 - 618
20	X-RAY DIFFRACTION	20	( CHAIN D AND RESID 1:7 )	D	1 - 7
21	X-RAY DIFFRACTION	21	( CHAIN D AND RESID 8:39 )	D	8 - 39

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