PDB-4hjg: Meditope-enabled trastuzumab

ID or keywords:

Entry

Database: PDB / ID: 4hjg

Title

Meditope-enabled trastuzumab

Components

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

Keywords

IMMUNE SYSTEM /

monoclonal antibody / cancer therapeutic

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: 2 Å

Authors

Donaldson, J.M. / Zer, C. / Avery, K.N. / Bzymek, K.P. / Horne, D.A. / 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	Oct 12, 2012	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

-
Download

PDBx/mmCIF format	4hjg.cif.gz	241.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4hjg.ent.gz	203.7 KB	Display	PDB format
PDBx/mmJSON format	4hjg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hj/4hjg ftp://data.pdbj.org/pub/pdb/validation_reports/hj/4hjg	HTTPS FTP

-
Related structure data

Related structure data	4gw1C 4gw5C 4hkzC 4ioiC 1n8z C: citing same article (ref.)
Similar structure data	4hkz-d 6b9z-d 5u5f-d 6o28-1 4ioi-d 6bae-d 6nt2-2 1men-d 6bah-d 6o2a-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

-
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 fragment

60.4 kDa, 4 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, 104.980, 117.820
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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
#4: Protein	Protein L fragment Mass: 6994.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Finegoldia magna (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q51918*PLUS
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 733 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.73 Å³/Da / Density % sol: 54.93 %
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

-
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: Dec 19, 2011
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: 2→33.55 Å / Num. all: 45516 / Num. obs: 44434 / % possible obs: 97.6 % / Observed criterion σ(F): 1.99 / Observed criterion σ(I): 2 / R_merge(I) obs: 0.049 / Net I/σ(I): 24.81
Reflection shell	Resolution: 2→2.05 Å / R_merge(I) obs: 0.236 / Mean I/σ(I) obs: 5.81 / % possible all: 90.7

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→33.545 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 17.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1947	2258	5.08 %
R_work	0.1532	-	-
obs	0.1552	44427	97.63 %
all	-	45526	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→33.545 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4205	0	0	733	4938

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4475
X-RAY DIFFRACTION	f_angle_d	1.065	6123
X-RAY DIFFRACTION	f_dihedral_angle_d	12.736	1662
X-RAY DIFFRACTION	f_chiral_restr	0.072	694
X-RAY DIFFRACTION	f_plane_restr	0.005	799

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 (%)
2-2.0435	0.2503	122	0.1834	2408	X-RAY DIFFRACTION	90
2.0435-2.0911	0.2881	146	0.2026	2544	X-RAY DIFFRACTION	96
2.0911-2.1433	0.197	127	0.1609	2600	X-RAY DIFFRACTION	97
2.1433-2.2013	0.2015	143	0.1552	2596	X-RAY DIFFRACTION	99
2.2013-2.266	0.2543	131	0.1828	2528	X-RAY DIFFRACTION	94
2.266-2.3392	0.2075	145	0.1663	2572	X-RAY DIFFRACTION	97
2.3392-2.4228	0.1833	130	0.1551	2648	X-RAY DIFFRACTION	98
2.4228-2.5197	0.2222	145	0.1556	2657	X-RAY DIFFRACTION	100
2.5197-2.6344	0.1925	153	0.1585	2633	X-RAY DIFFRACTION	99
2.6344-2.7732	0.2076	158	0.1621	2646	X-RAY DIFFRACTION	99
2.7732-2.9468	0.1811	163	0.1623	2649	X-RAY DIFFRACTION	99
2.9468-3.1742	0.206	129	0.1509	2691	X-RAY DIFFRACTION	99
3.1742-3.4933	0.182	146	0.1453	2670	X-RAY DIFFRACTION	99
3.4933-3.9981	0.1751	148	0.1381	2662	X-RAY DIFFRACTION	98
3.9981-5.0345	0.1542	130	0.1196	2776	X-RAY DIFFRACTION	99
5.0345-33.5497	0.1855	142	0.161	2889	X-RAY DIFFRACTION	99

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	0.2365	-0.4938	-0.024	2.149	2.2326	4.1848	0.0182	0.0026	0.0215	0.0831	0.0868	-0.0806	0.3835	0.1401	-0.0357	0.0949	-0.0013	0.0123	0.091	0.0031	0.1173	18.9199	-34.8797	-10.7167
2	2.6337	0.3978	-0.1787	2.4357	0.2969	1.6821	0.0169	-0.0278	-0.04	-0.072	-0.0368	0.0934	0.1106	-0.2196	-0.0016	0.0492	-0.012	0.0056	0.0982	-0.0039	0.0899	10.2476	-28.3895	-8.4484
3	0.6442	0.0065	0.4082	2.5326	2.417	4.3534	-0.0209	0.0066	-0.0535	-0.0945	-0.0315	-0.0017	-0.128	-0.1904	0.0564	0.0463	0.0071	-0.0016	0.1129	0.0137	0.078	15.3518	-26.4785	-10.6185
4	0.8155	-1.1628	-2.2962	1.6619	3.2728	6.4482	0.1139	0.0167	0.0204	0.0821	-0.0276	-0.0852	0.1352	-0.1414	-0.0679	0.0951	-0.0163	0.0211	0.0934	0.0101	0.0961	20.1746	-37.7891	-27.9201
5	3.5552	3.2992	-0.3839	6.8399	-0.9982	1.4202	0.0566	0.2371	0.4342	-0.5906	0.2668	0.1772	-0.4764	0.1172	-0.2506	0.3871	-0.0858	0.1224	0.1788	-0.0256	0.1832	31.6002	-19.0094	-49.0844
6	3.3435	2.4321	-1.9292	3.4481	-1.6021	2.7384	0.0623	-0.1807	-0.0542	0.0178	-0.0461	-0.2124	-0.1841	0.4095	0.0104	0.1383	-0.0048	0.0168	0.1727	-0.0445	0.0916	31.8417	-30.7412	-39.3139
7	3.3131	1.7786	-1.6627	2.7254	-0.7663	3.5484	0.1226	0.1614	0.0793	0.0919	0.0695	-0.1158	-0.1324	0.1516	-0.1839	0.1581	0.0184	-0.023	0.1049	-0.0382	0.085	29.105	-29.18	-35.4488
8	4.0295	2.0865	-2.2263	2.2202	-1.9183	2.854	0.1366	0.0677	0.0987	-0.2955	0.0643	-0.3072	-0.4093	0.5218	-0.0032	0.3144	-0.1083	0.1703	0.2765	-0.0897	0.2183	39.8997	-19.9133	-45.7182
9	2.2752	2.2336	-1.9478	3.8845	-2.1463	3.0617	-0.0677	0.1757	-0.0055	-0.3556	0.2744	-0.3991	-0.1785	0.1423	-0.1698	0.2315	-0.0259	0.0963	0.181	-0.0544	0.1756	35.2499	-32.5448	-48.2663
10	0.7774	-0.8042	-1.1976	2.2757	-0.0694	3.0316	-0.3302	0.5477	0.0306	-0.3372	0.3018	0.0836	-0.0719	-0.1549	0.0359	0.1094	0.0108	0.0043	0.0836	0.0143	0.0454	18.8507	-4.6201	-18.4019
11	5.8179	2.5403	-0.5441	2.1889	-1.455	1.4544	0.0604	0.0641	0.3773	0.04	0.134	0.256	-0.1341	-0.2525	-0.1735	0.0824	0.0311	0.0017	0.1103	0.0055	0.1655	8.2988	-4.0134	-11.212
12	1.5351	0.8976	-0.2158	2.342	-0.0134	1.7182	-0.0062	-0.0575	-0.0473	0.0645	0.0215	0.0203	-0.0172	-0.0064	-0.0068	0.0499	0.0023	0.0053	0.0815	0.0126	0.0781	16.9278	-8.9571	-8.2217
13	0.2794	0.0131	-0.0797	0.7063	0.6371	1.0419	0.0097	0.0368	-0.001	-0.4861	0.1301	-0.117	-0.4647	0.2338	-0.1205	0.258	-0.0418	0.055	0.1655	-0.018	0.1301	27.301	-14.4587	-38.4125
14	1.0763	0.8592	0.4159	2.3152	1.5254	2.5993	0.0319	-0.0411	0.1192	-0.2724	-0.0721	0.1781	-0.3247	-0.0398	0.0521	0.2165	0.0143	-0.0067	0.0998	-0.0126	0.1084	21.4766	-16.3997	-39.9149
15	1.7585	0.4865	1.1524	4.4896	3.8419	4.0205	-0.0356	0.1949	0.2682	-0.5815	0.0123	0.2647	-0.5821	0.0931	0.1203	0.6439	-0.0062	-0.0687	0.1132	0.0407	0.1762	20.5303	-10.0315	-46.7787
16	9.3662	0.2751	2.7406	8.7482	0.8879	1.4914	0.1825	-0.2608	-0.3144	0.6211	-0.0832	0.3426	-0.0351	-0.2205	-0.0737	0.3556	-0.0313	0.0734	0.4906	-0.012	0.4777	19.0807	13.2753	4.4958
17	6.596	2.5146	-5.7197	8.0404	0.4041	7.8105	0.2412	-0.5116	0.2846	0.6761	-0.2838	0.249	-0.026	0.004	0.0827	0.1965	-0.0389	-0.0302	0.1693	-0.0093	0.1169	29.2015	13.5052	-0.5536
18	4.5319	1.3507	-1.6337	1.4102	-0.6234	1.638	0.0049	-0.0771	0.1673	0.091	-0.0077	0.0412	-0.0483	0.0235	0.0081	0.1188	-0.0049	-0.0065	0.0678	-0.0157	0.1138	29.437	8.9334	-9.0209
19	6.108	-1.782	1.4578	1.6798	0.5198	4.1062	-0.0834	-0.6329	0.3154	0.4023	-0.088	-0.1641	-0.2791	-0.2363	0.175	0.2146	-0.0489	-0.0112	0.1729	-0.0327	0.1016	22.4123	2.855	0.4657
20	4.8311	-1.927	-0.786	3.3665	0.7355	4.8683	0.1291	-0.2665	0.0452	0.5675	-0.1593	-0.3572	0.3007	0.2161	0.0316	0.1982	-0.0248	-0.053	0.1276	0.0323	0.099	33.1913	3.9752	-0.5956
21	4.4861	3.7839	-0.8608	3.7411	0.9045	7.613	0.2169	-0.5111	-0.4067	0.3332	-0.1212	-0.7869	0.1747	0.8675	-0.0198	0.1381	0.003	-0.0831	0.2159	0.0128	0.3183	39.7395	4.5162	-6.5138
22	7.2837	4.6129	1.8344	5.5099	0.584	5.4816	0.0449	0.2201	0.0428	-0.4331	0.1197	-0.0242	0.1944	0.2492	-0.1322	0.2082	0.0605	-0.0105	0.0976	-0.0283	0.3036	25.6199	-43.9529	-15.3805
23	2.3369	0.0734	1.9362	2.8506	-0.1919	3.0709	0.2166	-0.2104	-0.4483	0.1048	-0.0165	-0.0877	0.2925	-0.032	-0.1531	0.1231	0.0142	-0.0271	0.143	0.0279	0.1993	25.0621	-43.4018	-8.0356
24	5.1796	3.4608	-0.0557	6.2614	1.0104	7.0995	0.0116	0.0734	-0.2944	-0.6825	0.3662	-0.2238	0.5419	0.9269	-0.1324	0.3473	0.0802	-0.0777	0.2717	0.0499	0.2706	29.2098	-48.7595	-12.6706

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 : 128 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 129 : 150 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 151 : 174 )
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 175 : 188 )
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESID 189 : 214 )
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESID 1 : 17 )
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESID 18 : 32 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 33 : 113 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 114 : 141 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 142 : 210 )
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 211 : 221 )
16	X-RAY DIFFRACTION	16	CHAIN H AND (RESID 1 : 7 )
17	X-RAY DIFFRACTION	17	CHAIN H AND (RESID 8 : 17 )
18	X-RAY DIFFRACTION	18	CHAIN H AND (RESID 18 : 32 )
19	X-RAY DIFFRACTION	19	CHAIN H AND (RESID 33 : 42 )
20	X-RAY DIFFRACTION	20	CHAIN H AND (RESID 43 : 47 )
21	X-RAY DIFFRACTION	21	CHAIN H AND (RESID 48 : 54 )
22	X-RAY DIFFRACTION	22	CHAIN E AND (RESID 20 : 33 )
23	X-RAY DIFFRACTION	23	CHAIN E AND (RESID 34 : 67 )
24	X-RAY DIFFRACTION	24	CHAIN E AND (RESID 68 : 81 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi