PDB-4gw1: cQFD Meditope

ID or keywords:

Entry

Database: PDB / ID: 4gw1

Title

cQFD Meditope

Components

Fab heavy chainFragment antigen-binding
Fab light chainFragment antigen-binding
cQFD meditope

Keywords

IMMUNE SYSTEM / IgG / EGFR

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta /

PHOSPHATE ION

Function and homology information

Biological species

Mus musculus (house mouse)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.24 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	Aug 31, 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
Revision 1.3	Apr 9, 2014	Group: Source and taxonomy
Revision 1.4	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.5	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gw1.cif.gz	360.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4gw1.ent.gz	294.8 KB	Display	PDB format
PDBx/mmJSON format	4gw1.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/gw/4gw1 ftp://data.pdbj.org/pub/pdb/validation_reports/gw/4gw1	HTTPS FTP

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Related structure data

Related structure data	4gw5C 4hjgC 4hkzC 4ioiC 1yy9S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5icz-2 5f88-2 5euk-1 6ayn-1 5etu-1 5hyq-1 5hyq-2 6au5-2 6axp-2 6azl-2 4msw-1 3d69-2 4dn3-d 5t1k-2 5f88-1 5icy-1 6azk-1 6azk-2 5t78-1 5id0-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#126 - Jun 2010 Epidermal Growth Factor similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Fab light chain

B: Fab heavy chain

C: Fab light chain

D: Fab heavy chain

E: cQFD meditope

F: cQFD meditope

hetero molecules

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

1

A: Fab light chain

B: Fab heavy chain

E: cQFD meditope

hetero molecules

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

2

C: Fab light chain

D: Fab heavy chain

F: cQFD meditope

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.257, 82.582, 211.630
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	Fab light chain / Fragment antigen-binding Mass: 23448.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus,Homo sapiens
#2: Antibody	Fab heavy chain / Fragment antigen-binding Mass: 23725.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus,Homo sapiens
#3: Protein/peptide	cQFD meditope Mass: 1472.756 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.89 Å³/Da / Density % sol: 57.37 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Cetuximab Fab (5 mg/mL) was mixed with individual meditopes at a 1:10 molar ratio. Co-crystals that diffracted beyond 2.2 were grown in 100 mM sodium phosphate/citrate, 2.5 M ...Details: Cetuximab Fab (5 mg/mL) was mixed with individual meditopes at a 1:10 molar ratio. Co-crystals that diffracted beyond 2.2 were grown in 100 mM sodium phosphate/citrate, 2.5 M sodium/potassium phosphate, and 1.6 % w/v meso-erythritol. The crystals were wicked through 14% (w/v) meso-erythritol and flash frozen in liquid nitrogen, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal

Density Matthews: 2.89 Å³/Da / Density % sol: 57.37 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Cetuximab Fab (5 mg/mL) was mixed with individual meditopes at a 1:10 molar ratio. Co-crystals that diffracted beyond 2.2 were grown in 100 mM sodium phosphate/citrate, 2.5 M ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.91837 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: 2010-02-20
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91837 Å / Relative weight: 1
Reflection	Resolution: 2.24→19.85 Å / Num. all: 55215 / Num. obs: 53800 / % possible obs: 97.4 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 17 / Redundancy: 4.2 %

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Processing

Software

Name	Version	Classification
Blu-Ice	ice	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1yy9

1yy9

Resolution: 2.24→19.85 Å / SU ML: 0.31 / σ(F): 1.99 / Phase error: 21.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2257	2728	5.07 %	random
R_work	0.1819	-	-	-
obs	0.1841	53791	97.58 %	-

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.526 Å² / k_sol: 0.4 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.4903 Å²	0 Å²	-0 Å²
2-	-	6.4266 Å²	-0 Å²
3-	-	-	-8.9169 Å²

Refinement step

Cycle: LAST / Resolution: 2.24→19.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6801	0	15	581	7397

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6980
X-RAY DIFFRACTION	f_angle_d	0.913	9485
X-RAY DIFFRACTION	f_dihedral_angle_d	11.321	2484
X-RAY DIFFRACTION	f_chiral_restr	0.062	1072
X-RAY DIFFRACTION	f_plane_restr	0.003	1211

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 (%)
2.24-2.2794	0.2848	105	0.2416	2347	X-RAY DIFFRACTION	85
2.2794-2.3232	0.3179	145	0.2366	2538	X-RAY DIFFRACTION	94
2.3232-2.3706	0.2635	159	0.2313	2682	X-RAY DIFFRACTION	99
2.3706-2.422	0.2755	151	0.2144	2690	X-RAY DIFFRACTION	100
2.422-2.4782	0.2772	138	0.2113	2713	X-RAY DIFFRACTION	100
2.4782-2.5401	0.2771	161	0.2052	2686	X-RAY DIFFRACTION	100
2.5401-2.6086	0.2945	110	0.1979	2755	X-RAY DIFFRACTION	100
2.6086-2.6852	0.2293	152	0.1929	2756	X-RAY DIFFRACTION	100
2.6852-2.7717	0.2422	161	0.1968	2665	X-RAY DIFFRACTION	100
2.7717-2.8705	0.2735	147	0.1947	2724	X-RAY DIFFRACTION	100
2.8705-2.985	0.2374	130	0.1921	2756	X-RAY DIFFRACTION	100
2.985-3.1204	0.2297	153	0.1891	2697	X-RAY DIFFRACTION	99
3.1204-3.2842	0.2339	150	0.1858	2706	X-RAY DIFFRACTION	99
3.2842-3.4889	0.1968	142	0.1683	2727	X-RAY DIFFRACTION	98
3.4889-3.7566	0.2159	144	0.1665	2718	X-RAY DIFFRACTION	98
3.7566-4.1316	0.2133	138	0.1542	2713	X-RAY DIFFRACTION	97
4.1316-4.7224	0.1573	142	0.1312	2693	X-RAY DIFFRACTION	97
4.7224-5.9234	0.1888	157	0.1561	2708	X-RAY DIFFRACTION	96
5.9234-19.8545	0.2257	143	0.2222	2789	X-RAY DIFFRACTION	94

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	4.0303	-2.6776	-1.0944	7.1498	2.9069	4.6711	-0.0252	0.1155	0.2804	0.4005	-0.0549	-0.3513	-0.4981	0.2607	0.1145	0.3231	-0.0781	0.0216	0.2564	0.0277	0.1987	12.6586	17.7183	20.8028
2	1.8977	-0.2738	0.5926	3.223	0.7262	3.0161	0.1001	0.0073	0.0948	-0.1504	-0.0626	-0.0113	-0.5199	0.1999	-0.0323	0.2614	-0.0294	0.0238	0.1687	0.0289	0.1406	5.2328	15.3805	13.6331
3	0.421	0.3161	0.4636	1.6452	2.694	4.3576	0.0063	0.1537	0.085	-0.1904	-0.0647	0.0059	-0.3836	-0.1238	0.0326	0.2916	-0.0246	0.0236	0.1792	0.0277	0.1779	6.7395	15.1924	22.6638
4	0.9782	-0.3855	0.8036	3.057	-1.9549	4.0442	0.0058	-0.1151	0.0246	0.0786	-0.0472	-0.097	0.1096	0.0913	0.0415	0.1164	0.0324	0.0093	0.1754	-0.0069	0.1816	5.7963	9.8155	54.0722
5	2.1561	1.4958	0.1756	3.5252	-1.0276	2.7864	0.1215	-0.1914	-0.0199	0.2077	-0.1289	-0.0959	0.0992	-0.0161	-0.0051	0.0624	0.0257	0.0064	0.2057	0.0006	0.1731	5.5415	13.0041	54.5519
6	3.4683	-1.1294	3.1442	2.2201	-2.0334	8.194	0.0493	-0.0447	-0.2218	0.0112	0.0256	0.2528	0.4179	-0.2004	-0.1058	0.1954	-0.0247	0.0504	0.2132	-0.0027	0.2221	-6.4622	-6.5489	20.058
7	2.4343	1.2096	1.8113	4.2895	2.8768	2.6001	-0.2087	0.2368	-0.0508	-0.0732	-0.1121	0.1122	0.0534	0.2926	0.1712	0.162	-0.0454	0.046	0.2158	-0.0014	0.1531	3.0115	-3.6232	14.9799
8	0.4053	-0.0205	-0.0424	0.2647	0.1221	4.0979	0.0059	0.0561	-0.1566	-0.0048	-0.0126	-0.0201	0.4935	0.1416	-0.0078	0.1833	0.0062	0.0152	0.127	0.0136	0.1961	-0.3199	-6.057	20.901
9	3.2962	-1.9435	0.4719	3.4166	-1.9703	1.3279	-0.242	-0.1689	0.4763	0.7197	0.2332	-0.2548	-0.2063	-0.0134	-0.0819	0.1057	-0.0302	-0.0173	0.2116	-0.0582	0.2546	-5.0264	10.2832	52.8556
10	0.5841	-0.5488	-0.2247	2.4507	0.3001	0.9449	-0.0104	0.027	0.1191	-0.0701	-0.0206	-0.1694	0.058	0.1461	0.0289	0.0899	0.0291	0.0142	0.1958	0.0565	0.1885	-4.047	5.861	43.5761
11	1.8814	-0.7997	0.2614	2.67	0.0208	1.0488	-0.1105	-0.0423	0.0441	0.2855	-0.0872	0.3246	0.0903	-0.2755	0.2533	0.122	-0.004	0.0112	0.2095	-0.0014	0.1963	-12.8264	2.8035	47.8977
12	3.5188	-2.7017	2.8279	8.076	-6.074	8.4823	0.2482	-0.1456	-0.3968	0.0446	0.1896	0.4441	0.5999	-0.5249	-0.428	0.3025	-0.1145	0.0416	0.2663	-0.0102	0.2506	20.3842	24.4517	17.7774
13	1.4416	0.5621	-0.1293	3.4843	-0.5455	3.5075	0.0114	0.0169	-0.152	0.0317	0.1326	-0.0777	0.4864	0.0263	-0.1413	0.2159	-0.0221	0.0346	0.1451	-0.0252	0.1117	28.3316	28.2763	12.9114
14	-0.0002	-0.0362	0.0777	1.7867	-3.9313	8.6477	-0.1728	0.1693	-0.0861	-0.4423	0.2628	-0.1348	-0.0062	-0.2425	-0.112	0.3317	-0.0807	0.0649	0.2014	-0.0517	0.1851	25.6439	20.5039	34.05
15	1.7228	-0.7072	-0.9783	2.4718	2.0772	3.142	-0.0611	-0.1179	-0.0752	0.095	0.0261	-0.0247	0.0478	0	0.0395	0.1108	0.024	-0.0055	0.1017	0.0314	0.1577	26.4361	35.4151	51.6518
16	1.66	0.111	-0.372	3.7626	2.3454	3.5366	-0.1481	-0.1703	-0.1185	0.2699	0.1131	-0.0443	0.2871	0.1594	0.0131	0.0973	0.0334	0.0306	0.149	0.0286	0.1532	26.8414	32.2175	52.6776
17	0.2182	-0.0187	-0.1732	0.1128	0.1388	5.1307	-0.0199	0.0255	0.1183	-0.0589	0.0005	0.0313	-0.4529	0.0383	0.0092	0.2071	-0.0244	0.0042	0.1587	-0.0059	0.2176	33.4099	48.5126	16.3796
18	3.0918	-2.1795	1.6172	4.1477	-0.7467	1.4475	0.048	-0.0555	-0.122	0.0942	-0.0033	0.0211	-0.0307	0.0398	-0.0653	0.0973	-0.0017	0.0432	0.1541	-0.0323	0.1316	39.1955	39.1194	44.4678
19	6.5241	0.0304	-4.1041	2.4505	-1.6501	8.254	0.2688	-0.399	-0.3429	1.0622	-0.1156	-0.4797	-0.4731	1.2478	-0.1484	0.375	-0.0312	-0.0466	0.3514	0.0127	0.2575	8.4848	6.3738	31.0396
20	2.0117	-1.6178	1.6524	1.6273	-1.2562	5.0176	-0.0412	-0.5489	-0.2356	1.461	-0.0093	0.8591	-0.3432	-1.0396	0.1456	0.5549	0.0079	0.2487	0.4829	0.0469	0.4285	24.4596	36.8542	28.7739

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 1:18)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 19:75)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 76:113)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 114:163)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 164:212)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 1:33)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 34:56)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 57:130)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 131:151)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 152:194)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 195:221)
12	X-RAY DIFFRACTION	12	CHAIN C AND (RESSEQ 1:25)
13	X-RAY DIFFRACTION	13	CHAIN C AND (RESSEQ 26:101)
14	X-RAY DIFFRACTION	14	CHAIN C AND (RESSEQ 102:113)
15	X-RAY DIFFRACTION	15	CHAIN C AND (RESSEQ 114:163)
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESSEQ 164:213)
17	X-RAY DIFFRACTION	17	CHAIN D AND (RESSEQ 1:130)
18	X-RAY DIFFRACTION	18	CHAIN D AND (RESSEQ 131:220)
19	X-RAY DIFFRACTION	19	CHAIN E AND (RESSEQ 1:12)
20	X-RAY DIFFRACTION	20	CHAIN F AND (RESSEQ 1:12)

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