PDB-8ib1: Structure of the LAH31 Fab bound to an influenza virus HA epitope...

ID or keywords:

Entry

Database: PDB / ID: 8ib1

Title

Structure of the LAH31 Fab bound to an influenza virus HA epitope peptide

Components

Hemagglutinin HA2 chain
LAH31 Fab heavy chain
LAH31 Fab light chain

Keywords

ANTIVIRAL PROTEIN / Antibody / Fab / Influenza / epitope

Function / homology

Function and homology information

viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Influenza A virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Suzuki, T. / Hashiguchi, T.

Funding support

Japan, 1items

Citation

Journal: Plos Pathog. / Year: 2023
Title: Structural basis for cross-group recognition of an influenza virus hemagglutinin antibody that targets postfusion stabilized epitope.
Authors: Tonouchi, K. / Adachi, Y. / Suzuki, T. / Kuroda, D. / Nishiyama, A. / Yumoto, K. / Takeyama, H. / Suzuki, T. / Hashiguchi, T. / Takahashi, Y.

History

Deposition	Feb 9, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 26, 2023	Provider: repository / Type: Initial release
Revision 1.1	Aug 30, 2023	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ib1.cif.gz	228.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8ib1.ent.gz	151.4 KB	Display	PDB format
PDBx/mmJSON format	8ib1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ib1_validation.pdf.gz	450.7 KB	Display	wwPDB validaton report
Full document	8ib1_full_validation.pdf.gz	453 KB	Display
Data in XML	8ib1_validation.xml.gz	20.4 KB	Display
Data in CIF	8ib1_validation.cif.gz	29.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ib/8ib1 ftp://data.pdbj.org/pub/pdb/validation_reports/ib/8ib1	HTTPS FTP

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Related structure data

Related structure data	5wl2S 6wrpS S: Starting model for refinement
Similar structure data	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) #76 - Apr 2006 Hemagglutinin similarity (5) #170 - Feb 2014 Broadly Neutralizing Antibodies similarity (5) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (5) #62 - Feb 2005 Major Histocompatibility Complex similarity (5) #63 - Mar 2005 T-Cell Receptor similarity (5) #200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

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)
#76 - Apr 2006
Hemagglutinin
similarity (5)
#170 - Feb 2014
Broadly Neutralizing Antibodies
similarity (5)
#259 - Jul 2021
Designed Proteins and Citizen Science
similarity (5)
#62 - Feb 2005
Major Histocompatibility Complex
similarity (5)
#63 - Mar 2005
T-Cell Receptor
similarity (5)
#200 - Aug 2016
Quasisymmetry in Icosahedral Viruses
similarity (1)

Deposited unit

A: LAH31 Fab light chain

B: LAH31 Fab heavy chain

C: Hemagglutinin HA2 chain

56.9 kDa, 3 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)	68.050, 86.510, 89.970
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

#1: Antibody	LAH31 Fab light chain Mass: 26441.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody	LAH31 Fab heavy chain Mass: 28766.678 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein/peptide	Hemagglutinin HA2 chain Mass: 1685.764 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: Q03909
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.33 Å³/Da / Density % sol: 47.15 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium acetate, Ammonium acetate, PEG4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.95→45.98 Å / Num. obs: 73864 / % possible obs: 98.7 % / Redundancy: 6.2 % / B_iso Wilson estimate: 25.79 Å² / CC_1/2: 0.994 / Net I/σ(I): 10
Reflection shell	Resolution: 1.95→2.06 Å / Num. unique obs: 5812 / CC_1/2: 0.654

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6WRP,5WL2

6wrp

5wl2

Resolution: 1.95→45.98 Å / SU ML: 0.2208 / Cross valid method: FREE R-VALUE / σ(F): 0.83 / Phase error: 23.4506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2252	3722	5.04 %
R_work	0.185	70142	-
obs	0.187	73864	98.15 %

Solvent computation

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

Displacement parameters

B_iso mean: 33.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→45.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3373	0	0	304	3677

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0047	3443
X-RAY DIFFRACTION	f_angle_d	0.7629	4677
X-RAY DIFFRACTION	f_chiral_restr	0.0521	534
X-RAY DIFFRACTION	f_plane_restr	0.0068	600
X-RAY DIFFRACTION	f_dihedral_angle_d	13.4118	1245

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 (%)
1.95-1.97	0.3688	98	0.3108	1987	X-RAY DIFFRACTION	75.79
1.97-2	0.3484	155	0.3009	2392	X-RAY DIFFRACTION	91.19
2-2.02	0.3306	157	0.2993	2465	X-RAY DIFFRACTION	94.01
2.02-2.05	0.2903	131	0.284	2525	X-RAY DIFFRACTION	95.33
2.05-2.08	0.2747	122	0.2532	2596	X-RAY DIFFRACTION	97.21
2.08-2.12	0.3263	149	0.2357	2618	X-RAY DIFFRACTION	99.03
2.12-2.15	0.2458	123	0.2168	2646	X-RAY DIFFRACTION	99.89
2.15-2.19	0.2269	132	0.208	2653	X-RAY DIFFRACTION	99.93
2.19-2.23	0.249	132	0.2135	2626	X-RAY DIFFRACTION	99.96
2.23-2.27	0.2599	128	0.208	2692	X-RAY DIFFRACTION	99.96
2.27-2.32	0.2076	142	0.1983	2624	X-RAY DIFFRACTION	99.93
2.32-2.37	0.2578	136	0.1954	2669	X-RAY DIFFRACTION	99.96
2.37-2.42	0.2519	144	0.1992	2620	X-RAY DIFFRACTION	100
2.42-2.48	0.2521	142	0.1989	2672	X-RAY DIFFRACTION	99.86
2.48-2.55	0.2613	159	0.1976	2621	X-RAY DIFFRACTION	99.78
2.55-2.62	0.2466	147	0.2013	2652	X-RAY DIFFRACTION	99.71
2.62-2.71	0.2182	115	0.1927	2636	X-RAY DIFFRACTION	99.46
2.71-2.81	0.221	135	0.1794	2647	X-RAY DIFFRACTION	99.86
2.81-2.92	0.2217	133	0.1861	2647	X-RAY DIFFRACTION	100
2.92-3.05	0.2375	133	0.1748	2656	X-RAY DIFFRACTION	99.96
3.05-3.21	0.2279	175	0.1684	2631	X-RAY DIFFRACTION	100
3.21-3.41	0.201	137	0.1649	2640	X-RAY DIFFRACTION	99.96
3.41-3.68	0.1721	123	0.1518	2662	X-RAY DIFFRACTION	99.93
3.68-4.05	0.2232	154	0.1556	2644	X-RAY DIFFRACTION	99.89
4.05-4.63	0.1439	133	0.144	2641	X-RAY DIFFRACTION	99.89
4.63-5.83	0.2133	154	0.1596	2628	X-RAY DIFFRACTION	99.96
5.83-45.98	0.2246	133	0.195	2652	X-RAY DIFFRACTION	99.39

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	1.59481769185	0.692282866378	0.663198929111	3.01574734723	0.915751095607	1.70565332324	0.245316031336	0.0815362006645	-0.515236965052	0.241416640065	-0.196400557763	-0.197548384281	0.145190278135	-0.0646593031537	-0.0200113074212	0.132041336711	0.0190608422183	-0.00922452032555	0.228819613685	-0.0432012698151	0.467234997641	35.8450217916	11.7206263618	46.3095180559
2	3.15210388497	0.870284138581	0.885375594092	0.724439129473	-0.251832587998	1.17013502811	0.095574158651	0.249056812445	-0.317280886899	-0.0846950861659	-0.0263189584581	-0.231922182951	0.0358233373361	0.0837471254881	-0.0714347734447	0.153190415961	0.00399145846757	-0.0251820354048	0.145958458041	-0.0181160168865	0.321549924242	24.2837024754	10.0683095641	45.8121439998
3	4.45751359274	1.29726850749	0.639420057276	3.32246909967	-0.279023997337	2.9865979726	0.0412560490015	0.255596148647	0.447850731733	0.0748264654724	0.0982094620439	-0.0233609930433	-0.25487425458	0.144186390279	-0.0467043776669	0.145821375307	0.0129302234677	0.0133527416576	0.19175813395	0.0214722195289	0.369317454476	21.4566818165	20.1278847841	42.9944937267
4	3.41459641477	1.15728620182	0.126893133707	1.15174112319	-0.0429743669299	0.635669726003	0.0649042475	0.119281245747	-0.384665862091	-0.108145287555	0.0157973506278	-0.121288620149	0.0457766924876	-0.00740663682098	-0.0975270142507	0.152567581816	0.019254143668	0.00157743845443	0.14185410739	-0.0111209315848	0.317798398303	31.1876836589	14.5211681078	47.8359169594
5	2.46808312089	0.0336371565542	-0.667914027439	1.6956603371	-0.757258400205	5.95734312966	0.0474929191263	-0.238314122121	-0.0682649258841	0.2784203111	0.0938913203864	-0.187029280273	0.418670436113	0.472493772148	-0.0470281061402	0.234838119213	0.0460496901609	-0.0563410819971	0.22164154931	-0.0119224006489	0.266045254145	48.1413679912	22.5168789063	76.0052772642
6	1.73834848705	-0.354177975546	0.6783956178	1.62804327615	-0.0627128946584	4.86410993365	-0.0318251033473	-0.0694227241078	0.0301512268363	0.353804906663	0.15252386434	-0.234831724673	0.376262043316	0.804660818824	-0.0978017919797	0.256530628636	0.092985530567	-0.0356737636061	0.338727165029	-0.0500426855548	0.296668593431	51.4847367526	21.1029231441	74.8306079903
7	1.02552409231	-0.476278956187	0.819520321973	1.00289308771	-0.559977504781	2.13297563458	0.0997538693068	-0.0712795155316	-0.222580239554	0.180817651859	0.000605934240262	0.0875504914064	0.0602045828334	-0.0735219438245	-0.121943642887	0.186311457105	-0.0445611642854	-0.0294461354803	0.16434339473	0.0383336381355	0.346703724615	15.14113277	5.32815526307	62.3720062824
8	1.18711772516	-0.438626126382	1.32831025719	2.6572615111	0.618508967194	2.86318661632	0.186491734163	-0.139157018007	-0.0802173826942	0.509979647114	0.0725019696843	-0.159514867434	0.227663715435	8.80247505201E-5	-0.22488655938	0.252323015508	0.007668955384	0.0572322007489	0.185230229448	-0.018671088705	0.248021041782	34.1451156257	18.7494363797	79.0092675908
9	2.21743218545	-0.370420110319	0.363486758341	1.34196541818	0.308328681164	2.82259691747	0.0703291296412	-0.0257752859274	0.242261307814	0.0469706430035	-0.0803990524404	0.143827119389	0.256434378825	-0.122257318344	0.0304133666621	0.211911716052	-0.0265417978959	0.0170843987519	0.161345689769	-0.0336111271974	0.233432599981	35.1343410152	23.4699750082	74.7737798963
10	4.13547455312	2.43894801374	-0.370858476286	8.85058026466	0.469419315808	4.40983141285	0.247864051226	-0.19447894175	0.692195753207	0.905166395114	-0.368131142513	0.856642752397	0.155161174783	-0.443921349633	0.0793819599815	0.257960444328	-0.0194733936512	0.0615328670884	0.267372021965	-0.0911485066077	0.315526624932	30.9873643226	29.200191885	81.6864848584
11	7.8855059595	9.13344317265	-5.11778549769	2.00015627244	-5.83007526144	3.82807055501	-0.368893893324	0.469033614026	-0.190537435913	-0.524162283228	0.115451159209	-0.909335181603	0.345279791399	0.135975103815	0.122524392658	0.307111082662	-0.023898775798	-0.141596484667	0.24550010566	-0.0436595836151	0.578502788848	7.07299338873	-1.63846399074	45.4149715241
12	1.03804124957	2.40920225661	-0.0366554919491	5.88950646441	1.21069244423	9.65715139153	0.0900421377977	0.143590499527	-0.718321390021	-0.120327984177	-0.0957301213173	0.199788210031	0.206026010507	-0.793643383409	-0.115696365453	0.165121039532	-0.0117508075279	-0.080307635742	0.271550013422	0.0360887189364	0.449739297543	5.0227753032	4.06866061617	45.5893420257

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 26 through 43 )	A	A	26 - 43	1 - 18
2	2	chain 'A' and (resid 44 through 78 )	A	A	44 - 78	19 - 53
3	3	chain 'A' and (resid 79 through 91 )	A	A	79 - 91	54 - 66
4	4	chain 'A' and (resid 92 through 144 )	A	A	92 - 144	67 - 119
5	5	chain 'A' and (resid 145 through 181 )	A	A	145 - 181	120 - 156
6	6	chain 'A' and (resid 182 through 243 )	A	A	182 - 243	157 - 218
7	7	chain 'B' and (resid 27 through 136 )	B	B	27 - 136	1 - 110
8	8	chain 'B' and (resid 137 through 179 )	B	B	137 - 179	111 - 148
9	9	chain 'B' and (resid 180 through 222 )	B	B	180 - 222	149 - 191
10	10	chain 'B' and (resid 223 through 247 )	B	B	223 - 247	192 - 216
11	11	chain 'C' and (resid 1 through 5 )	C	C	1 - 5	1 - 5
12	12	chain 'C' and (resid 6 through 13 )	C	C	6 - 13	6 - 13

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