PDB-4ioi: Meditope-enabled trastuzumab in complex with CQFDLSTRRLKC

ID or keywords:

Entry

Database: PDB / ID: 4ioi

Title

Meditope-enabled trastuzumab in complex with CQFDLSTRRLKC

Components

Immunoglobulin G-binding protein A
Protein L
Trastuzumab heavy chain
Trastuzumab light chain
meditope

Keywords

IMMUNE SYSTEM / monoclonal antibody / cancer immunotherapy

Function / homology

Function and homology information

IgG binding / immunoglobulin binding / extracellular region
Similarity search - Function

Biological species

Homo sapiens (human)

Staphylococcus aureus (bacteria)

Finegoldia magna (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Bzymek, K.P. / Zer, C. / Avery, K.N. / Williams, J.C.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Identification and grafting of a unique peptide-binding site in the Fab framework of monoclonal antibodies.
Authors: Donaldson, J.M. / Zer, C. / Avery, K.N. / Bzymek, K.P. / Horne, D.A. / Williams, J.C.

History

Deposition	Jan 7, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 9, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2013	Group: Database references
Revision 1.2	Nov 6, 2013	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ioi.cif.gz	243.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4ioi.ent.gz	205 KB	Display	PDB format
PDBx/mmJSON format	4ioi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ioi_validation.pdf.gz	445.1 KB	Display	wwPDB validaton report
Full document	4ioi_full_validation.pdf.gz	448.5 KB	Display
Data in XML	4ioi_validation.xml.gz	27.7 KB	Display
Data in CIF	4ioi_validation.cif.gz	41.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/io/4ioi ftp://data.pdbj.org/pub/pdb/validation_reports/io/4ioi	HTTPS FTP

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Related structure data

Related structure data	4gw1C 4gw5C 4hjgC 4hkzC C: citing same article (ref.)
Similar structure data	5u5f-d 5u6a-d 6b9y-d 6bae-d 4hkz-d 5u5m-d 6b9z-d 6bah-d 4hjg-d 4bj6-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #211 - Jul 2017 Pilus Machine similarity (4)

Deposited unit

A: Trastuzumab light chain

B: Trastuzumab heavy chain

H: Immunoglobulin G-binding protein A

E: Protein L

C: meditope

61.9 kDa, 5 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)	53.310, 105.110, 117.620
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Antibody , 3 types, 3 molecules ABH

#1: Antibody	Trastuzumab light chain Mass: 23502.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#2: Antibody	Trastuzumab heavy chain Mass: 23774.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse)
#3: Antibody	Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A Mass: 6124.607 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: spa, SAV0111 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A015

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Protein / Protein/peptide / Non-polymers , 3 types, 543 molecules EC

#4: Protein	Protein L Mass: 6994.734 Da / Num. of mol.: 1 / Mutation: T34I, D55A, Y73N, T74H, I75M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Finegoldia magna (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q51918
#5: Protein/peptide	meditope Mass: 1472.756 Da / Num. of mol.: 1 / Source method: obtained synthetically
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.66 Å³/Da / Density % sol: 53.81 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 20% PEG 3350, 25 mM NaCl, 50 mM Hepes, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 1, 2012
Radiation	Monochromator: Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.95→33.58 Å / Num. all: 48788 / Num. obs: 44759 / % possible obs: 91.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / R_merge(I) obs: 0.047 / Net I/σ(I): 23.6
Reflection shell	Resolution: 1.95→2 Å / Redundancy: 4.4 % / R_merge(I) obs: 0.452 / Mean I/σ(I) obs: 3.4 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
CrystalClear		data collection
MOLREP		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→33.579 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 20.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2044	2246	5.02 %
R_work	0.1757	-	-
obs	0.1772	44750	91.76 %
all	-	48788	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→33.579 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4295	0	0	541	4836

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4548
X-RAY DIFFRACTION	f_angle_d	1.09	6211
X-RAY DIFFRACTION	f_dihedral_angle_d	12.502	1676
X-RAY DIFFRACTION	f_chiral_restr	0.077	702
X-RAY DIFFRACTION	f_plane_restr	0.005	811

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 (%)
1.95-1.9957	0.2658	167	0.2225	2795	X-RAY DIFFRACTION	98
1.9957-2.0421	0.228	162	0.192	2833	X-RAY DIFFRACTION	100
2.0421-2.0931	0.2524	131	0.1832	2864	X-RAY DIFFRACTION	100
2.0931-2.1497	0.2181	136	0.184	2861	X-RAY DIFFRACTION	100
2.1497-2.213	0.2576	150	0.2227	2817	X-RAY DIFFRACTION	98
2.213-2.2844	0.4327	70	0.365	1157	X-RAY DIFFRACTION	41
2.2844-2.366	0.2773	134	0.2228	2662	X-RAY DIFFRACTION	93
2.366-2.4607	0.2233	155	0.1943	2872	X-RAY DIFFRACTION	100
2.4607-2.5727	0.217	156	0.1857	2866	X-RAY DIFFRACTION	100
2.5727-2.7082	0.2184	146	0.1832	2887	X-RAY DIFFRACTION	100
2.7082-2.8778	0.255	149	0.175	2893	X-RAY DIFFRACTION	100
2.8778-3.0999	0.1914	164	0.175	2903	X-RAY DIFFRACTION	100
3.0999-3.4116	0.1801	143	0.1621	2899	X-RAY DIFFRACTION	100
3.4116-3.9046	0.1825	60	0.1515	1146	X-RAY DIFFRACTION	39
3.9046-4.9169	0.162	162	0.1291	2961	X-RAY DIFFRACTION	100
4.9169-33.5835	0.1527	161	0.1672	3088	X-RAY DIFFRACTION	100

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	0.4136	0.7355	0.3042	4.3789	-3.5755	5.7835	0.0651	-0.019	-0.0164	0.1322	-0.0046	0.1058	0.269	0.0035	-0.0931	0.1777	0.0116	0.0273	0.1827	0.0007	0.2124	-18.857	-34.8353	10.3026
2	2.1321	-0.3818	-0.2695	2.1223	-0.3588	0.8066	-0.059	0.0359	-0.1638	0.1214	0.0381	-0.1524	0.0964	0.3001	0.0248	0.1348	0.0184	0.007	0.2004	-0.0018	0.1931	-10.3013	-28.6022	8.3032
3	0.8552	-0.6001	0.2575	3.9177	-2.5296	3.864	-0.052	-0.0868	-0.0317	0.1869	0.007	-0.0995	0.0068	0.1513	0.0602	0.1323	0.0018	-0.0084	0.1771	-0.0099	0.1532	-15.1751	-26.7098	10.562
4	-0.0202	0.0523	-0.0984	2.5657	-4.9373	9.4755	-0.0018	0.0835	0.0238	-0.2872	-0.089	-0.2675	0.6305	-0.0999	0.0551	0.2668	0.0201	0.0404	0.177	0.0133	0.1774	-20.073	-37.5814	27.5564
5	2.7921	-2.3698	-0.9118	5.9041	1.2247	1.8699	0.1488	-0.0189	0.2367	0.3382	0.1663	0.2294	-0.5333	-0.4457	-0.2666	0.4087	0.0676	0.1063	0.287	0.0867	0.2445	-31.8609	-26.1079	42.7201
6	3.7375	0.792	-3.4818	1.2834	-0.1823	3.5537	0.1302	-0.0942	-0.2127	0.0351	0.2023	0.6787	-0.1742	-0.7171	-0.3052	0.289	0.0708	0.0898	0.4867	0.1949	0.4874	-39.9452	-27.5266	38.8944
7	8.1049	-4.621	-5.8954	4.812	3.3502	6.3208	0.1021	-0.2962	0.0545	0.2763	0.2669	0.3844	-0.4087	-0.1678	-0.3352	0.3094	0.0564	0.0927	0.2678	0.0916	0.28	-30.5794	-25.2807	39.1772
8	4.2097	-3.9664	-3.7649	7.0761	4.8622	6.3321	0.0206	-0.1172	0.1144	0.535	0.2971	0.4243	-0.2462	-0.4468	-0.3122	0.3994	0.0634	0.1146	0.3127	0.1105	0.3002	-35.1715	-32.7585	47.9066
9	1.5462	-0.0724	-1.5099	1.8916	0.3225	2.7858	-0.4359	-0.6254	0.0374	0.4667	0.3147	-0.1294	-0.0908	0.1117	0.1161	0.2675	0.0009	-0.0189	0.1563	-0.0164	0.1718	-18.584	-4.9058	18.3067
10	8.0783	-4.702	-0.4226	4.5515	1.3388	2.7128	0.0121	0.2281	0.2204	0.0427	0.0517	-0.4222	-0.0487	0.3902	-0.0553	0.1701	-0.0303	-0.0072	0.2163	-0.0165	0.2541	-8.1118	-4.1823	11.2654
11	3.7044	1.4669	-2.1367	4.8161	-2.5493	3.8595	0.0914	0.1096	0.0516	-0.0167	0.1827	0.223	0.1094	0.0964	-0.2981	0.1412	0.0405	0.0062	0.1767	-0.027	0.1745	-18.5073	-12.3873	7.6531
12	8.0451	0.0388	-2.5426	2.1193	0.8003	3.9949	0.2749	0.8511	0.1242	-0.3126	-0.1374	0.0201	-0.0807	-0.2509	-0.1076	0.2598	0.0675	-0.0105	0.1983	0.022	0.1573	-18.9088	-5.5324	0.199
13	2.9822	-1.0021	-0.6466	3.0786	0.0667	1.9728	0.014	0.0663	-0.0914	0.0989	0.0391	-0.2811	-0.0997	0.179	-0.0375	0.1668	0.0054	-0.0332	0.1815	-0.0212	0.1747	-14.9129	-8.0784	10.0711
14	0.0915	0.2708	0.0264	0.8321	0.7215	3.1693	-0.0628	0.0306	0.0328	0.3399	0.0291	0.1516	-0.2064	-0.2391	0.0125	0.3181	0.0672	0.0603	0.2041	0.0292	0.1926	-27.4262	-6.525	24.579
15	0.6667	-0.4422	0.0664	2.9141	-1.6283	3.0182	0.0454	-0.0391	-0.094	0.4834	-0.0532	-0.0268	-0.588	0.0355	-0.0193	0.431	0.0005	-0.0166	0.2264	0.0266	0.2303	-23.5049	-18.9161	40.7097
16	1.9843	-1.898	2.139	2.4324	-3.6672	6.6746	-0.0207	-0.0609	0.2152	1.114	-0.0695	-0.4558	-1.0584	0.325	0.1062	0.7751	-0.0602	-0.0766	0.2641	0.0054	0.3092	-18.8536	-11.1898	44.2724
17	2.7364	-0.9747	-5.0076	9.0297	1.2598	9.3089	0.6752	1.0485	0.5723	-1.3526	-0.4661	-0.958	-0.472	0.4252	-0.1927	0.5216	0.09	0.0464	0.4962	0.0872	0.3795	-24.691	13.5465	-2.0198
18	5.2798	-2.1566	-1.6998	3.7446	0.9794	3.6556	0.1663	0.2796	0.0151	-0.4464	-0.1767	0.188	-0.1062	-0.2013	0.0068	0.2866	0.054	-0.0269	0.1752	0.0089	0.1758	-30.111	6.055	4.7632
19	6.7794	-4.2694	1.5543	6.5782	0.7021	5.6984	0.2856	-0.2276	0.2184	0.3951	-0.2037	0.1057	0.3528	-0.3173	-0.0986	0.3699	-0.0983	0	0.1994	0.0265	0.486	-25.5548	-44.2868	15.2089
20	6.9133	-1.3934	2.798	4.6598	-0.1689	4.9219	0.192	0.4126	-0.3001	-0.1224	-0.1855	0.327	0.2437	0.048	-0.0201	0.2028	-0.0301	0.0023	0.177	-0.0259	0.2855	-25.1525	-41.6248	8.3197
21	3.3854	-5.0648	-2.068	8.669	1.8453	2.8718	0.0735	0.0109	-0.8112	0.3196	0.0585	0.8459	0.7481	-0.2028	-0.1364	0.6104	-0.0534	-0.1756	0.3528	-0.1013	0.6287	-26.5256	-52.1394	8.9725
22	2.4217	-4.0212	2.0215	9.2918	-1.1414	5.7205	0.2875	-0.3676	-0.1059	0.4687	0.2989	-0.0951	0.4766	-0.6656	-0.5586	0.5153	-0.0819	-0.1058	0.3263	-0.02	0.3875	-27.9913	-48.8735	12.5585
23	4.9971	-0.469	-0.0843	2.1093	-0.2751	6.3452	-0.0569	-0.3643	-0.2393	0.9071	0.1813	0.6914	-0.3206	-0.544	0.0116	0.3337	0.061	0.1071	0.2391	0.0324	0.3171	-25.0398	-23.0974	20.9535

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 1 : 25 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 26 : 75 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 76 : 101 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 102 : 113 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 114 : 150 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 151 : 163 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 164 : 188 )
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 189 : 214 )
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESID 1 : 17 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 18 : 32 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 33 : 52 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 53 : 67 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 68 : 110 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 111 : 126 )
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 127 : 195 )
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 196 : 220 )
17	X-RAY DIFFRACTION	17	CHAIN H AND (RESID 2 : 16 )
18	X-RAY DIFFRACTION	18	CHAIN H AND (RESID 17 : 54 )
19	X-RAY DIFFRACTION	19	CHAIN E AND (RESID 19 : 33 )
20	X-RAY DIFFRACTION	20	CHAIN E AND (RESID 34 : 61 )
21	X-RAY DIFFRACTION	21	CHAIN E AND (RESID 62 : 69 )
22	X-RAY DIFFRACTION	22	CHAIN E AND (RESID 70 : 81 )
23	X-RAY DIFFRACTION	23	CHAIN C AND (RESID 1 : 12 )

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