PDB-7jp4: Crystal structure of a refolded head domain hemagglutinin HA from...

ID or keywords:

Entry

Database: PDB / ID: 7jp4

Title

Crystal structure of a refolded head domain hemagglutinin HA from Influenza A virus A/Fort Monmouth/1/1947

Components

Hemagglutinin

Keywords

VIRAL PROTEIN /

National Institute of Allergy and Infectious Disease / NIAID /

influenza virus / flu /

vaccine / seasonal flu / refolded protein /

head domain /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / host cell surface receptor binding / apical plasma membrane / 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
Similarity search - Function

Biological species

Influenza A virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Sci Rep / Year: 2023
Title: Structural characterisation of hemagglutinin from seven Influenza A H1N1 strains reveal diversity in the C05 antibody recognition site.
Authors: Ghafoori, S.M. / Petersen, G.F. / Conrady, D.G. / Calhoun, B.M. / Stigliano, M.Z.Z. / Baydo, R.O. / Grice, R. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E. / Forwood, J.K.

History

Deposition	Aug 7, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 27, 2021	Provider: repository / Type: Initial release
Revision 1.1	May 24, 2023	Group: Database references / Category: citation / citation_author / database_2 Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7jp4.cif.gz	185.3 KB	Display	PDBx/mmCIF format
PDB format	pdb7jp4.ent.gz	144.6 KB	Display	PDB format
PDBx/mmJSON format	7jp4.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/jp/7jp4 ftp://data.pdbj.org/pub/pdb/validation_reports/jp/7jp4	HTTPS FTP

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Related structure data

Related structure data	6d8wC 6ml8C 6myaC 6n41SC 6onaC 6osrC 7jpdC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4tkg-4 4yys-2 5ja7-1 6kyc-d 5erc-d 1h2f-d 6btn-1 4yys-1 1pmj-d 3uyx-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 - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: InvbN.18715.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#221 - May 2018 Human Papillomavirus and Vaccines 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

#221 - May 2018
Human Papillomavirus and Vaccines
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: Hemagglutinin

B: Hemagglutinin

hetero molecules

53 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hemagglutinin

hetero molecules

defined by author
Evidence: gel filtration
26.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Hemagglutinin

hetero molecules

defined by author
26.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.250, 59.950, 66.540
Angle α, β, γ (deg.)	90.000, 95.060, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Hemagglutinin / Mass: 26305.434 Da / Num. of mol.: 2 / Fragment: Head domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Fort Monmouth/1/1947(H1N1)) Strain: A/Fort Monmouth/1/1947(H1N1) / Gene: HA / Production host: Escherichia coli (E. coli) / References: UniProt: Q20MG8
#2: Chemical	ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID / MOPS Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₅NO₄S / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.94 Å³/Da / Density % sol: 36.6 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: InvbN.18715.a.TK11.PD38383 at 5.04 mg/mL against Morpheus screen condition H5 with 10% PEG 20000, 20% PEG 550 MME, 0.1 M MOPS/Hepes pH 7.5, 0.02 M glutamate, 0.02 M alanine, 0.02 M glycine, ...Details: InvbN.18715.a.TK11.PD38383 at 5.04 mg/mL against Morpheus screen condition H5 with 10% PEG 20000, 20% PEG 550 MME, 0.1 M MOPS/Hepes pH 7.5, 0.02 M glutamate, 0.02 M alanine, 0.02 M glycine, 0.02 M lysine, 0.02 M serine; crystal tracking ID 311819h5, unique puck ID awm9-4

Crystal

Density Matthews: 1.94 Å³/Da / Density % sol: 36.6 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: InvbN.18715.a.TK11.PD38383 at 5.04 mg/mL against Morpheus screen condition H5 with 10% PEG 20000, 20% PEG 550 MME, 0.1 M MOPS/Hepes pH 7.5, 0.02 M glutamate, 0.02 M alanine, 0.02 M glycine, ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 9, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 2→33.14 Å / Num. obs: 27217 / % possible obs: 99.6 % / Redundancy: 4.165 % / B_iso Wilson estimate: 30.212 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.094 / R_rim(I) all: 0.108 / Χ²: 1.019 / Net I/σ(I): 11.56 / Num. measured all: 113371 / Scaling rejects: 5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2-2.05	4.178	0.529	3.09	8389	2009	2008	0.886	0.609	100
2.05-2.11	4.221	0.441	3.65	8129	1925	1926	0.902	0.507	100
2.11-2.17	4.205	0.384	4.41	8094	1931	1925	0.918	0.443	99.7
2.17-2.24	4.202	0.347	4.8	7846	1872	1867	0.935	0.399	99.7
2.24-2.31	4.218	0.313	5.21	7533	1790	1786	0.941	0.359	99.8
2.31-2.39	4.224	0.283	5.9	7304	1734	1729	0.953	0.325	99.7
2.39-2.48	4.214	0.232	6.86	6983	1660	1657	0.967	0.266	99.8
2.48-2.58	4.199	0.185	8.16	6798	1626	1619	0.975	0.213	99.6
2.58-2.7	4.215	0.164	9.15	6558	1559	1556	0.983	0.188	99.8
2.7-2.83	4.226	0.123	11.67	6166	1472	1459	0.988	0.141	99.1
2.83-2.98	4.189	0.1	13.45	5873	1414	1402	0.992	0.116	99.2
2.98-3.16	4.177	0.079	15.96	5513	1328	1320	0.995	0.091	99.4
3.16-3.38	4.134	0.063	19.19	5126	1246	1240	0.994	0.073	99.5
3.38-3.65	4.131	0.054	22.01	4916	1193	1190	0.997	0.062	99.7
3.65-4	4.094	0.047	23.99	4393	1079	1073	0.997	0.054	99.4
4-4.47	4.113	0.042	26.53	4010	978	975	0.998	0.048	99.7
4.47-5.16	4.029	0.04	27.6	3473	871	862	0.998	0.046	99
5.16-6.32	3.913	0.042	25.9	2872	739	734	0.996	0.049	99.3
6.32-8.94	3.907	0.04	26.79	2231	578	571	0.997	0.047	98.8
8.94-33.14	3.66	0.033	28.57	1164	331	318	0.999	0.039	96.1

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.18.2-3874-000	refinement
PDB_EXTRACT	3.25	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6n41

6n41

Resolution: 2→33.14 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.86 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2257	1335	4.91 %
R_work	0.1909	25861	-
obs	0.1926	27196	99.52 %

Solvent computation

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

Displacement parameters

B_iso max: 82.91 Å² / B_iso mean: 28.5299 Å² / B_iso min: 12.47 Å²

Refinement step

Cycle: final / Resolution: 2→33.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3266	0	26	211	3503
B_iso mean	-	-	21.2	31.75	-
Num. residues	-	-	-	-	411

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3404
X-RAY DIFFRACTION	f_angle_d	0.809	4633
X-RAY DIFFRACTION	f_dihedral_angle_d	21.468	1229
X-RAY DIFFRACTION	f_chiral_restr	0.049	479
X-RAY DIFFRACTION	f_plane_restr	0.005	594

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2-2.07	0.2638	157	0.2262	2555	2712	100
2.07-2.15	0.268	118	0.2122	2586	2704	100
2.15-2.25	0.2949	132	0.2175	2575	2707	100
2.25-2.37	0.2773	151	0.2219	2564	2715	100
2.37-2.52	0.3051	121	0.2164	2576	2697	100
2.52-2.71	0.3074	129	0.2198	2602	2731	99
2.71-2.99	0.2552	142	0.2015	2560	2702	99
2.99-3.42	0.2143	117	0.1897	2603	2720	99
3.42-4.31	0.1682	140	0.161	2595	2735	100
4.31-33.14	0.1798	128	0.167	2645	2773	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	1.134	-0.4674	1.3651	1.8797	0.2572	3.9252	-0.025	-0.1579	-0.0461	0.2354	0.0649	-0.0948	0.2851	0.0415	-0.0224	0.1706	-0.0019	0.0149	0.1976	0.0486	0.1816	-22.0027	26.2247	10.4364
2	4.2244	-0.0696	-1.9672	2.4707	-0.3132	2.1083	-0.0814	-0.0684	-0.038	-0.158	-0.0728	-0.0981	-0.0333	0.1535	0.0087	0.1947	0.0244	-0.0041	0.0929	0.0339	0.1625	-22.2669	31.9012	1.2617
3	6.6554	0.352	0.7145	3.3784	-0.5909	4.327	0.0257	1.1161	-0.2079	-0.4047	-0.0999	-0.4833	0.0819	0.3416	0.0669	0.2533	-0.0073	0.0493	0.3254	-0.0313	0.2394	5.932	11.6358	16.9552
4	6.6807	-0.3026	1.259	0.8417	-1.2219	2.382	-0.1324	0.7638	0.1079	-0.2086	0.1071	-0.1869	-0.1461	0.3157	0.0355	0.2729	-0.0477	0.0147	0.311	0.0069	0.2071	2.0125	13.1905	19.859
5	5.3211	1.6769	-0.6721	3.2438	-1.0159	3.4089	0.2307	-0.0298	-0.458	0.1728	-0.1302	-0.4687	0.0975	0.401	-0.0818	0.1607	0.0447	-0.0291	0.2819	-0.0264	0.1727	3.7566	3.3413	29.4155
6	3.3301	0.5412	0.3861	2.2335	0.1874	2.2649	-0.0415	0.333	-0.4727	-0.1488	0.1146	0.0413	0.3437	0.2009	-0.1077	0.1616	0.0194	-0.0315	0.1981	-0.0167	0.227	-12.7145	-1.8823	23.5499
7	5.9945	0.941	2.9749	1.0499	0.1753	3.1843	-0.0801	-0.2867	0.1337	0.1157	0.0098	0.1456	-0.1473	-0.3004	0.0973	0.1725	0.0329	0.0244	0.1521	0.0057	0.149	-12.2818	8.4128	31.8946
8	8.2069	-1.5078	-4.0574	6.791	0.8577	6.9547	-0.0977	0.0919	0.6137	-0.5186	0.4105	0.0824	-0.0857	-0.0304	-0.2257	0.2858	-0.0754	-0.083	0.3767	0.1153	0.2819	-19.3085	12.6737	15.1017
9	2.346	0.219	2.5294	1.6278	-1.278	4.1299	0.0454	-0.1937	-0.0755	0.1816	0.0563	0.0867	-0.2162	-0.2381	-0.0647	0.1715	0.0366	0.0164	0.1971	-0.0307	0.1579	-6.088	11.235	32.9142
10	2.0522	-1.1688	-0.1147	0.8671	-0.4017	3.7978	-0.0724	0.1395	-0.1086	0.1265	0.0187	-0.1118	-0.1302	0.1332	0.0713	0.1507	0.018	-0.0085	0.0722	0.0296	0.1887	-2.8353	6.1597	29.536
11	1.9693	-0.7347	-0.7188	2.4073	0.1879	5.1544	0.0559	0.1757	0.0857	-0.2623	0.0452	-0.2205	0.0831	0.7637	-0.1168	0.2503	0.0271	-0.0197	0.3938	-0.0247	0.2331	-10.3961	25.3946	-0.5731
12	5.0803	-1.996	-1.7803	7.5104	3.4872	8.6082	0.2652	0.6173	-0.2344	-0.7165	0.0204	-0.3939	-0.3669	0.1563	-0.2729	0.2269	-0.0522	-0.0053	0.2763	-0.0128	0.2223	-16.8295	30.0296	-8.8882
13	2.7967	-0.5679	1.1739	2.0506	0.4183	5.5178	-0.0025	0.1515	0.3644	-0.0536	-0.0708	-0.209	-0.662	0.3655	0.0412	0.2788	-0.0424	-0.0092	0.1955	0.0253	0.1971	-18.2801	40.3642	9.1009
14	1.8801	-0.076	1.0002	1.0545	0.8806	5.9712	-0.0419	-0.0824	0.0322	0.0532	0.056	0.1089	-0.6076	-0.3564	0.0901	0.2387	0.0558	0.0033	0.1851	0.0437	0.2064	-28.2803	36.9811	5.8451
15	1.8958	-0.2154	1.0256	2.3047	-0.6597	5.0795	-0.2043	-0.3837	-0.0203	0.4637	0.0953	0.0346	0.4941	0.2425	0.0789	0.1561	0.0621	0.0055	0.2036	0.0343	0.1715	-23.0584	30.4151	15.0245
16	1.8644	-0.0655	1.85	3.5572	3.8036	8.5825	0.1452	-0.4064	-0.1335	0.4873	-0.2725	0.2357	0.7484	-0.8663	-0.0573	0.2553	-0.0833	0.0405	0.3616	0.0936	0.2577	-31.7999	26.3846	11.9856

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 214 through 246 )	B	214 - 246
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 247 through 261 )	B	247 - 261
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 50 through 64 )	A	50 - 64
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 65 through 106 )	A	65 - 106
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 107 through 123 )	A	107 - 123
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 124 through 162 )	A	124 - 162
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 163 through 213 )	A	163 - 213
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 214 through 227 )	A	214 - 227
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 228 through 246 )	A	228 - 246
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 247 through 261 )	A	247 - 261
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 50 through 106 )	B	50 - 106
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 107 through 117 )	B	107 - 117
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 118 through 149 )	B	118 - 149
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 150 through 173 )	B	150 - 173
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 174 through 194 )	B	174 - 194
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 195 through 213 )	B	195 - 213

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