PDB-5otj: Monomeric polcalcin (Phl p 7) in complex with two identical aller...

ID or keywords:

Entry

Database: PDB / ID: 5otj

Title

Monomeric polcalcin (Phl p 7) in complex with two identical allergen-specific antibodies

Components

(102.1F10 Fab ...) x 2
Polcalcin Phl p 7

Keywords

IMMUNE SYSTEM /

Fab /

allergen /

antibody / IgE / polcalcin

Function / homology

Function and homology information

calcium ion binding
Similarity search - Function

Biological species

Homo sapiens (human)

Phleum pratense (timothy grass)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Mitropoulou, A.N. / Davies, A.M. / Beavil, A.J. / McDonnell, J.M. / Sutton, B.J.

Funding support

United Kingdom, 2items

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structure of a patient-derived antibody in complex with allergen reveals simultaneous conventional and superantigen-like recognition.
Authors: Mitropoulou, A.N. / Bowen, H. / Dodev, T.S. / Davies, A.M. / Bax, H.J. / Beavil, R.L. / Beavil, A.J. / Gould, H.J. / James, L.K. / Sutton, B.J.

History

Deposition	Aug 22, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 5, 2018	Provider: repository / Type: Initial release
Revision 1.1	Sep 19, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0	Mar 11, 2020	Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1	Jan 17, 2024	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_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5otj.cif.gz	388.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5otj.ent.gz	316.8 KB	Display	PDB format
PDBx/mmJSON format	5otj.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/ot/5otj ftp://data.pdbj.org/pub/pdb/validation_reports/ot/5otj	HTTPS FTP

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Related structure data

Related structure data	1rzfS 3h42S S: Starting model for refinement
Similar structure data	2bdn-d 3pnw-6 2x7l-3 6was-1 6pe9-4 5x0t-1 6bit-1 5x0t-2 3pnw-7 3skj-2 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 - 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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

L: 102.1F10 Fab light chain

H: 102.1F10 Fab heavy chain

A: 102.1F10 Fab light chain

D: Polcalcin Phl p 7

B: 102.1F10 Fab heavy chain

C: Polcalcin Phl p 7

hetero molecules

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

1

L: 102.1F10 Fab light chain

H: 102.1F10 Fab heavy chain

C: Polcalcin Phl p 7

hetero molecules

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

2

A: 102.1F10 Fab light chain

D: Polcalcin Phl p 7

B: 102.1F10 Fab heavy chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	52.760, 178.671, 66.070
Angle α, β, γ (deg.)	90.00, 94.82, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules DC

#3: Protein	Polcalcin Phl p 7 / Calcium-binding pollen allergen Phl p 7 / P7 Mass: 12234.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phleum pratense (timothy grass) / Production host: Escherichia coli (E. coli) / References: UniProt: O82040

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Antibody , 2 types, 4 molecules LAHB

#1: Antibody	102.1F10 Fab light chain Mass: 22769.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: pyroglutamate instead of glutamine at position 1 of chains L and A Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293F / Production host: Homo sapiens (human)
#2: Antibody	102.1F10 Fab heavy chain Mass: 24701.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK-293F / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 273 molecules

#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₂H₆O₂
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.6 Å³/Da / Density % sol: 52.65 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 15% PEG 6000 5% MPD

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.35→61.78 Å / Num. obs: 46391 / % possible obs: 91.8 % / Redundancy: 2.3 % / CC_1/2: 0.984 / R_merge(I) obs: 0.104 / Net I/σ(I): 5.7
Reflection shell	Resolution: 2.35→2.43 Å / Redundancy: 2 % / R_merge(I) obs: 0.591 / Mean I/σ(I) obs: 2 / Num. unique obs: 4267 / CC_1/2: 0.512 / % possible all: 92

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3H42 1RZF

3h42

1rzf

Resolution: 2.35→52.999 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.63

	R_factor	Num. reflection	% reflection
R_free	0.2345	1973	4.31 %
R_work	0.1994	-	-
obs	0.2008	45772	90.49 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.35→52.999 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7423	0	20	265	7708

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7646
X-RAY DIFFRACTION	f_angle_d	0.527	10432
X-RAY DIFFRACTION	f_dihedral_angle_d	11.879	4522
X-RAY DIFFRACTION	f_chiral_restr	0.043	1177
X-RAY DIFFRACTION	f_plane_restr	0.004	1353

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 (%)
2.35-2.4088	0.3202	126	0.2761	2929	X-RAY DIFFRACTION	85
2.4088-2.4739	0.3109	128	0.2632	2948	X-RAY DIFFRACTION	86
2.4739-2.5467	0.3	167	0.2605	3121	X-RAY DIFFRACTION	91
2.5467-2.6289	0.3123	146	0.2513	3257	X-RAY DIFFRACTION	94
2.6289-2.7229	0.3391	149	0.2545	3236	X-RAY DIFFRACTION	94
2.7229-2.8319	0.2486	139	0.2504	3207	X-RAY DIFFRACTION	93
2.8319-2.9607	0.2587	144	0.2239	3183	X-RAY DIFFRACTION	92
2.9607-3.1168	0.2652	146	0.2257	3161	X-RAY DIFFRACTION	91
3.1168-3.3121	0.3005	130	0.2215	3152	X-RAY DIFFRACTION	91
3.3121-3.5677	0.2224	142	0.1863	3154	X-RAY DIFFRACTION	92
3.5677-3.9267	0.1896	139	0.1739	3150	X-RAY DIFFRACTION	91
3.9267-4.4946	0.2009	137	0.1604	3113	X-RAY DIFFRACTION	90
4.4946-5.6617	0.1759	140	0.1543	3072	X-RAY DIFFRACTION	89
5.6617-53.0123	0.1859	140	0.172	3116	X-RAY DIFFRACTION	89

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	0.0394	-0.0022	-0.0235	0.0068	-0.0106	0.0303	-0.0466	-0.0794	0.0128	-0.0213	0.1676	-0.0476	0.0353	-0.2008	0.0003	0.196	-0.0027	0.0313	0.1632	-0.0025	0.1799	25.1576	47.7435	-83.6544
2	0.0017	0.0039	-0.0038	0.0018	0.0036	0.0102	0.0736	0.0047	0.0858	-0.0521	0.0444	-0.1147	-0.0354	0.0493	0.0011	0.164	-0.0125	-0.0004	0.071	-0.0021	0.1126	36.1475	53.1691	-88.4978
3	0.0148	-0.0141	0.0039	0.017	-0.0156	0.0206	0.0107	-0.0444	0.0261	0.0949	0.1046	0.0257	-0.0506	0.0008	0.022	0.156	0.0123	-0.0732	0.0971	-0.0272	0.1874	36.3813	46.1213	-79.2351
4	0.0043	-0.0158	0.0026	0.0684	0.0411	0.0226	0.0627	-0.0081	0.0611	0.0225	0.1641	0.0437	-0.0104	-0.0209	0.0217	0.2916	0.0121	-0.0018	0.0896	-0.05	0.1818	31.3474	52.8172	-83.3933
5	0.0085	-0.0128	-0.0029	0.0149	-0.0118	-0.0007	-0.0668	-0.0698	-0.0344	0.0937	0.1285	-0.0628	-0.0643	-0.0724	0.001	0.2211	-0.0038	0.0021	0.1898	-0.0368	0.1341	22.1625	59.2139	-88.3384
6	0.0018	-0.0057	0.0002	0.068	-0.0014	0.004	-0.003	0.0137	-0.002	-0.0562	0.042	0.0161	-0.0009	-0.0072	0.0001	0.0861	-0.0151	-0.0196	0.3148	0.0669	0.1268	1.5723	72.5112	-109.1043
7	0.0119	-0.0002	-0.0076	0.0131	-0.0083	0.0157	-0.0445	0.0285	-0.0172	-0.0639	0.1113	0.022	0.1263	-0.0508	0.0098	0.1647	0.0154	-0.0386	0.1634	0.0156	0.1312	13.1388	67.5829	-92.018
8	0.0299	-0.0314	-0.0409	0.1464	0.1415	0.1758	0.0292	0.0139	-0.0848	-0.0466	0.093	0.0087	0.2991	0.028	0.0305	0.2973	-0.0731	-0.0187	0.1508	0.0028	0.1003	10.1235	65.9626	-96.0658
9	0.0212	-0.0035	0.0046	0.0076	-0.0015	0.0019	-0.0134	0.0477	-0.0215	0.0247	0.0258	-0.0004	0.0319	-0.0453	-0.002	-0.1147	-0.0065	-0.082	0.2178	0.0631	0.2879	4.4585	67.4017	-88.6417
10	0.0455	0.0067	-0.0244	0.0247	0.0019	0.3798	-0.0541	0.0941	-0.0605	-0.1054	0.0306	-0.3312	-0.3395	-0.1674	0.0132	0.1828	-0.0152	0.042	0.1261	-0.0214	0.1985	37.4368	47.7761	-104.516
11	0.0908	0.0311	-0.0289	0.0675	-0.0731	0.0636	0.069	-0.022	0.0301	0.1092	-0.0684	0.0526	0.0383	0.2205	0.0047	0.1417	0.0277	0.0292	0.1728	0.0289	0.0785	13.2348	80.8313	-104.3919
12	0.0826	0.0362	-0.0978	0.0219	-0.0554	0.1483	-0.0739	0.0629	0.0291	-0.0522	0.0864	-0.0406	0.0587	-0.3288	0.0116	0.1041	0.0881	-0.0307	0.1413	-0.0556	0.1426	27.3988	11.9449	-75.8203
13	0.1649	-0.0393	-0.0147	0.0331	-0.0231	0.1004	-0.1351	0.1465	-0.019	-0.0684	0.1242	-0.1335	0.008	-0.3101	-0.0502	-0.233	0.2193	0.1404	0.1357	-0.1301	0.1468	29.5707	9.8365	-77.0817
14	0.0534	-0.0398	-0.0251	0.0661	0.0116	0.1132	-0.0597	-0.1296	0.0263	0.02	0.0885	-0.0019	-0.1421	0.0305	0.0014	0.0663	0.0033	0.0214	0.1981	-0.0409	0.131	4.9202	-5.3568	-68.8797
15	0.0029	0.0026	-0.006	0.0036	-0.0056	0.006	-0.0791	-0.0475	0.0154	-0.0147	-0.0275	-0.044	0.0052	-0.0268	-0	0.3545	0.0235	-0.0621	0.1567	-0.0392	0.3087	36.3103	42.6432	-69.7808
16	0.018	0.0108	0.0412	-0.0009	0.0137	0.0944	0.0555	0.006	0.0033	-0.0102	0.0792	-0.0866	-0.0559	0.0616	0.0349	0.3344	-0.0545	-0.0523	0.0601	-0.0373	0.3838	45.5469	32.8915	-65.0464
17	0.0274	-0.0088	0.0308	0.0063	0.0087	0.1727	0.0909	-0.1097	0.0957	-0.0482	0.0486	0.0528	0.0391	0.0695	0.0471	0.4927	0.064	0.0292	0.163	-0.1087	0.2139	34.5271	37.1296	-59.5238
18	0.0411	-0.0866	-0.0637	0.2862	0.1426	0.2328	-0.0323	-0.2664	0.1335	0.4413	0.0131	-0.2566	0.3223	-0.2671	-0.0495	0.1286	0.256	0.0108	-0.0872	-0.1595	0.076	32.8084	13.6062	-55.3475
19	0.1472	-0.0391	0.0199	0.0891	-0.099	0.1204	0.11	-0.1068	-0.1527	-0.217	-0.1227	0.0232	0.2242	0.3863	-0.0581	0.2307	0.0133	-0.0045	0.2135	-0.0614	0.0243	7.7263	-18.5452	-59.6115
20	0.0083	-0.0021	0.003	0.0012	-0.0001	0.0019	-0.0097	-0.0045	0.0008	-0.0095	-0.0093	-0.0244	0.0086	0.0364	-0.0124	0.4366	-0.0313	0.2159	0.2154	-0.0938	0.4025	38.6631	15.0205	-91.9319
21	0.0002	0.0017	-0.0009	0.0004	-0.0039	0.006	-0.0218	-0.0335	-0.0181	0.0406	-0.0022	0.017	0.0336	-0.0446	-0	0.2516	0.0325	0.0118	0.1008	-0.0187	0.3457	41.5443	24.7187	-87.5411
22	0.0622	0.0252	-0.0431	0.0157	-0.0269	0.0474	-0.021	0.027	-0.0175	-0.0079	-0.0878	-0.0408	0.0226	-0.0311	-0.0162	0.2419	0.0427	0.0877	0.1493	-0.0311	0.4189	48.4633	30.3976	-95.7955
23	0.0098	0.0055	0.0205	0.0346	0.0193	0.0445	0.0275	0.113	-0.0661	-0.0175	0.0306	0.0207	0.0259	0.0412	0.013	0.4232	0.0015	-0.0426	0.1073	-0.0962	0.2323	37.7716	24.3321	-100.0701

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'L' and (resid 2 through 35 )
2	X-RAY DIFFRACTION	2	chain 'L' and (resid 36 through 50 )
3	X-RAY DIFFRACTION	3	chain 'L' and (resid 51 through 71 )
4	X-RAY DIFFRACTION	4	chain 'L' and (resid 72 through 94 )
5	X-RAY DIFFRACTION	5	chain 'L' and (resid 95 through 123 )
6	X-RAY DIFFRACTION	6	chain 'L' and (resid 124 through 134 )
7	X-RAY DIFFRACTION	7	chain 'L' and (resid 135 through 155 )
8	X-RAY DIFFRACTION	8	chain 'L' and (resid 156 through 202 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 203 through 214 )
10	X-RAY DIFFRACTION	10	chain 'H' and (resid 1 through 119 )
11	X-RAY DIFFRACTION	11	chain 'H' and (resid 120 through 222 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 2 through 50 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 51 through 118 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 119 through 214 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 3 through 21 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 22 through 47 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 48 through 71 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 1 through 119 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 120 through 222 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 3 through 12 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 13 through 32 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 33 through 47 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 48 through 71 )

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Protein , 1 types, 2 molecules DC

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Antibody , 2 types, 4 molecules LAHB

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Non-polymers , 3 types, 273 molecules

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