PDB-7rcr: Crystal Structure of the refolded Hemagglutinin head domain of In...

ID or keywords:

Entry

Database: PDB / ID: 7rcr

Title

Crystal Structure of the refolded Hemagglutinin head domain of Influenza A virus A/Ohio/09/2015

Components

Hemagglutinin

Keywords

VIRAL PROTEIN / SSGCID /

Hemagglutinin /

Influenza A / Ohio/09/2015 /

head domain / refolded /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / 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: 1.6 Å

Authors

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

Citation

Journal: to be published
Title: Crystal Structure of the refolded Hemagglutinin head domain of Influenzavirus A Influenza A virus A/Ohio/09/2015
Authors: Abendroth, J. / Habrukowich, C.L. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Jul 8, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 4, 2021	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7rcr.cif.gz	127 KB	Display	PDBx/mmCIF format
PDB format	pdb7rcr.ent.gz	79.4 KB	Display	PDB format
PDBx/mmJSON format	7rcr.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/rc/7rcr ftp://data.pdbj.org/pub/pdb/validation_reports/rc/7rcr	HTTPS FTP

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Related structure data

Similar structure data	3uyw-4 3qqi-1 3mlh-2 4ynm-2 6y73-3 2zqu-d 7kkp-2 6y4y-4 6nqi-1 4li6-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#76 - Apr 2006 Hemagglutinin similarity (6) #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

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	36.670, 61.120, 89.340
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Hemagglutinin / Mass: 24101.965 Da / Num. of mol.: 1 / Fragment: InvbR.18715.a.TK11 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Ohio/09/2015 / Gene: HA / Plasmid: InvbR.18715.a.TK11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6C0TB04
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 269 / 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: 1.96 Å³/Da / Density % sol: 37.3 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: RigakuReagents JCSG+ screen, condition a10: 200mM potassium formate, 20% (w/V) PEG 3350: InvbR.18715.a.TK11.PD38402 at 4.1mg/ml: tray: 314055a1: cryo: 20% EG: puck vjj0-9.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 4, 2021 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. obs: 27045 / % possible obs: 99.2 % / Redundancy: 5.99 % / B_iso Wilson estimate: 21.663 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.074 / R_rim(I) all: 0.081 / Χ²: 0.93 / Net I/σ(I): 16.87

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.6-1.64	6.005	0.597	3.4	1968	0.859	0.656	99.9
1.64-1.69	6.04	0.467	4.39	1945	0.902	0.512	99.9
1.69-1.74	6.016	0.404	5.17	1885	0.93	0.444	100
1.74-1.79	6.052	0.323	6.35	1831	0.954	0.355	99.9
1.79-1.85	6.059	0.262	7.86	1755	0.969	0.288	99.8
1.85-1.91	6.018	0.212	9.3	1707	0.979	0.233	99.6
1.91-1.98	5.977	0.152	12.26	1651	0.989	0.167	99.7
1.98-2.07	6.029	0.127	14.31	1600	0.991	0.139	99.8
2.07-2.16	6.005	0.105	17.04	1541	0.992	0.115	99.5
2.16-2.26	5.983	0.088	19.12	1458	0.995	0.097	99.6
2.26-2.39	6.001	0.08	20.77	1398	0.995	0.088	99.6
2.39-2.53	6.017	0.073	22.99	1337	0.996	0.08	99.4
2.53-2.7	6.04	0.063	25.43	1231	0.996	0.069	98.4
2.7-2.92	6.009	0.054	28.03	1173	0.997	0.06	98.9
2.92-3.2	5.967	0.046	31.75	1069	0.998	0.051	98.6
3.2-3.58	5.95	0.04	35.75	984	0.999	0.043	98.2
3.58-4.13	5.917	0.037	38.83	854	0.998	0.041	97.3
4.13-5.06	5.819	0.032	40.6	742	0.999	0.035	97.2
5.06-7.16	5.746	0.032	40.05	579	0.999	0.035	96.5
7.16-50	5.264	0.03	39.16	337	0.999	0.034	92.6

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19 dev_4274	refinement
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 6uynA as per Morda

Resolution: 1.6→36.06 Å / SU ML: 0.1719 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.6678
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1997	1937	7.16 %	0
R_work	0.1597	25106	-	-
obs	0.1626	27043	99.23 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 17.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→36.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1649	0	4	269	1922

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0074	1777
X-RAY DIFFRACTION	f_angle_d	0.9172	2439
X-RAY DIFFRACTION	f_chiral_restr	0.0602	258
X-RAY DIFFRACTION	f_plane_restr	0.0069	319
X-RAY DIFFRACTION	f_dihedral_angle_d	11.5389	658

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 (%)
1.6-1.64	0.2499	136	0.2349	1768	X-RAY DIFFRACTION	99.79
1.64-1.68	0.2436	132	0.2036	1785	X-RAY DIFFRACTION	99.95
1.68-1.73	0.255	146	0.1949	1772	X-RAY DIFFRACTION	100
1.73-1.79	0.2335	131	0.1767	1784	X-RAY DIFFRACTION	99.9
1.79-1.85	0.2334	137	0.1699	1771	X-RAY DIFFRACTION	99.84
1.85-1.93	0.2093	153	0.1699	1776	X-RAY DIFFRACTION	99.54
1.93-2.02	0.1912	147	0.159	1748	X-RAY DIFFRACTION	99.84
2.02-2.12	0.1543	141	0.1512	1796	X-RAY DIFFRACTION	99.59
2.12-2.25	0.2028	141	0.1445	1789	X-RAY DIFFRACTION	99.54
2.26-2.43	0.1785	125	0.1533	1804	X-RAY DIFFRACTION	99.59
2.43-2.67	0.1943	118	0.1668	1811	X-RAY DIFFRACTION	98.92
2.67-3.06	0.2118	144	0.1631	1815	X-RAY DIFFRACTION	98.84
3.06-3.85	0.1893	122	0.1377	1821	X-RAY DIFFRACTION	97.88
3.86-36.06	0.1897	164	0.1543	1866	X-RAY DIFFRACTION	96.35

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	1.94183036536	-0.800992411928	0.258710922078	2.79939621271	-0.00729449658866	3.34275499308	0.0264432681872	-0.201453502522	-0.226936573915	0.226607223944	-0.0227718079108	0.123691040105	0.511465933285	-0.161958175227	-0.00878351371175	0.147933388087	-0.0226861193937	0.00704569697493	0.114291645649	0.0250038249854	0.139126691554	0.540899855338	-11.1439235503	14.907752572
2	1.01418733693	-0.448965614533	1.17506284989	0.730671475042	0.235712878377	3.0829906863	0.133857489699	-0.0540555757024	-0.228675125517	0.0858894507899	-0.0576376647483	-0.0422014670428	0.380890374455	0.0310111040492	-0.0646424554179	0.141389952171	-0.00758132586165	-0.00186843060931	0.132456510628	0.0147778907656	0.182544441353	5.32346243743	-10.7960181904	7.73536826171
3	2.3129061315	-0.866270403994	0.211031862924	1.44445849215	-0.0895048061422	2.5483962234	-0.0789064084065	-0.314794249283	0.0616689735045	0.124221899003	0.0540059048095	-0.185579937962	-0.0191784372783	0.284252496001	0.0286922020294	0.121049678584	-0.0211789259107	-0.0150414966039	0.0734747133182	0.00334542224013	0.12815687181	4.0159471859	-1.36102639962	15.8998612245
4	0.150964283154	-0.597831458674	-0.0738885519049	2.60728025996	0.279024667632	0.744328157095	0.0446953788475	0.0311798780024	-0.0706226183634	-0.129032854806	-0.0579102823314	0.242552689697	0.0147696270078	-0.148009577623	0.0141064363789	0.0575135091553	-0.0153136856409	0.0109674719573	0.0935038943598	-0.00926312480603	0.129900434599	-14.4436141666	-3.97860115248	2.13350608144
5	1.30273547886	-0.589688335772	0.832990220697	2.5803533374	-0.898454216834	2.05626715149	0.0481398040742	0.0444158479414	-0.0324594542142	-0.179390936171	-0.0713804887843	0.235094931238	0.0880242027911	-0.201407140789	-0.0192334787023	0.0560529348042	0.00265007716131	-0.0128225036966	0.0928406650066	-0.0282538908054	0.113539100562	-13.5792584409	0.517886609537	-2.7542281949
6	0.91466497804	-0.021205404749	0.252449971239	1.78065184188	1.55820937175	3.09401628009	0.0336731634325	0.0634544297143	-0.0178578308062	-0.138364349177	-0.0231103973334	0.0733941642647	-0.0941581893584	-0.0250638539621	-0.00456196371529	0.0573417960715	-0.000121087391552	0.00387242136167	0.0381121291372	0.0161519183122	0.0676950180639	-6.3102400274	4.92314548683	-0.8749137245
7	4.40292435461	2.1617615309	2.78626642034	5.69281603835	3.66275525781	2.95462854975	0.00693715196161	0.106190845415	-0.123206697953	-0.000739263571852	0.109305791064	-0.382706408371	-0.101933176268	0.340523186977	-0.0970899448333	0.0992904288419	-0.0225057555906	0.00515253780618	0.0888971429928	0.00327043797786	0.102550839109	1.77743094478	11.6516532338	2.08469742718
8	0.718752461325	-0.490784064638	0.05089738824	3.02713712598	1.630746997	1.81222262161	0.0633803712817	0.0559803685945	-0.0413061405814	-0.156615175953	-0.0655718405823	-0.0343418471056	-0.0788972682768	0.0245682243771	-0.0218164307464	0.0439610504515	-0.00818887017998	0.0168023833528	0.0594142573001	0.0125932739225	0.0674084828572	-0.396633419975	1.93635805021	-0.687255742517
9	0.78284529416	0.0784711337424	-0.0586367623884	1.87914784073	-0.107539769057	3.07581404239	0.0601316938266	-0.0426589580054	-0.0298269635756	0.10300864964	-0.0136928003926	-0.0388687614758	0.118429822044	0.0608657378334	-0.0754519315605	0.0422237118321	-0.00194068873459	-0.000782941010878	0.0429753200949	-0.0121466458537	0.085022578019	-4.8718051474	2.36583432672	8.68989348734

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

ID	Refine TLS-ID	Selection details	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 64 through 93 )	64 - 93	1 - 26
2	2	chain 'A' and (resid 94 through 114 )	94 - 114	27 - 47
3	3	chain 'A' and (resid 115 through 132 )	115 - 132	48 - 65
4	4	chain 'A' and (resid 133 through 160 )	133 - 160	66 - 93
5	5	chain 'A' and (resid 161 through 177 )	161 - 177	94 - 110
6	6	chain 'A' and (resid 178 through 215 )	178 - 215	111 - 148
7	7	chain 'A' and (resid 216 through 227 )	216 - 227	149 - 160
8	8	chain 'A' and (resid 228 through 261 )	228 - 261	161 - 194
9	9	chain 'A' and (resid 262 through 276 )	262 - 276	195 - 209

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