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- PDB-6mzk: Crystal structure of hemagglutinin from influenza virus A/Pennsyl... -

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Basic information

Entry
Database: PDB / ID: 6mzk
TitleCrystal structure of hemagglutinin from influenza virus A/Pennsylvania/14/2010 (H3N2)
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / crystal structure hemagglutinin influenza H3N2 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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
Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsDai, Y.N. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: to be published
Title: Crystal structure of hemagglutinin from influenza virus A/Pennsylvania/14/2010 (H3N2)
Authors: Dai, Y.N. / Fremont, D.H.
History
DepositionNov 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,48118
Polymers168,2543
Non-polymers5,22715
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20630 Å2
ΔGint53 kcal/mol
Surface area57550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.720, 394.900, 102.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-773-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 324 or resid 336...
21(chain B and (resid 8 through 324 or resid 336...
31(chain C and (resid 8 through 500 or resid 702 through 703 or resid 706 or resid 707))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 8 through 324 or resid 336...A8 - 324
121(chain A and (resid 8 through 324 or resid 336...A336 - 500
131(chain A and (resid 8 through 324 or resid 336...A8 - 708
141(chain A and (resid 8 through 324 or resid 336...A702
211(chain B and (resid 8 through 324 or resid 336...B8 - 324
221(chain B and (resid 8 through 324 or resid 336...B336 - 500
231(chain B and (resid 8 through 324 or resid 336...B700 - 702
241(chain B and (resid 8 through 324 or resid 336...B707
251(chain B and (resid 8 through 324 or resid 336...B701
311(chain C and (resid 8 through 500 or resid 702 through 703 or resid 706 or resid 707))C8 - 500
321(chain C and (resid 8 through 500 or resid 702 through 703 or resid 706 or resid 707))C702 - 703
331(chain C and (resid 8 through 500 or resid 702 through 703 or resid 706 or resid 707))C706
341(chain C and (resid 8 through 500 or resid 702 through 703 or resid 706 or resid 707))C707

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Components

#1: Protein Hemagglutinin /


Mass: 56084.668 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: E9P7B6
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.12 Å3/Da / Density % sol: 75.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M Mes pH 6.5, 1.2M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: NOIR-1 / Detector: CMOS / Date: May 30, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.5→49.56 Å / Num. obs: 119566 / % possible obs: 100 % / Redundancy: 43 % / Biso Wilson estimate: 50.09 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.436 / Net I/σ(I): 15.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 41.5 % / Rmerge(I) obs: 8.689 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5835 / CC1/2: 0.366 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YP5

2yp5


Resolution: 2.5→49.556 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.5
RfactorNum. reflection% reflection
Rfree0.2306 5971 5 %
Rwork0.2071 --
obs0.2083 119355 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.94 Å2 / Biso mean: 61.5912 Å2 / Biso min: 21.85 Å2
Refinement stepCycle: final / Resolution: 2.5→49.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11516 0 341 219 12076
Biso mean--86.99 53.16 -
Num. residues----1450
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7167X-RAY DIFFRACTION10.222TORSIONAL
12B7167X-RAY DIFFRACTION10.222TORSIONAL
13C7167X-RAY DIFFRACTION10.222TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.52840.38471850.35993634381997
2.5284-2.55820.37742080.34483717392599
2.5582-2.58940.40171850.34593736392199
2.5894-2.62210.36981840.327537663950100
2.6221-2.65660.33222140.329336853899100
2.6566-2.6930.36332010.340937533954100
2.693-2.73150.37911980.320537093907100
2.7315-2.77230.31381950.30537903985100
2.7723-2.81560.33042070.283737323939100
2.8156-2.86170.31991910.269137683959100
2.8617-2.91110.30421910.269737803971100
2.9111-2.9640.28421980.252537353933100
2.964-3.0210.30861890.246837923981100
3.021-3.08270.27511930.239737643957100
3.0827-3.14970.24862030.221737353938100
3.1497-3.22290.24712120.213338004012100
3.2229-3.30350.23122190.211137593978100
3.3035-3.39280.20311990.198237233922100
3.3928-3.49260.20712040.194237863990100
3.4926-3.60530.21091950.174137873982100
3.6053-3.73410.17321860.175837853971100
3.7341-3.88360.18382020.17137973999100
3.8836-4.06030.17582290.168837814010100
4.0603-4.27420.19422050.157437893994100
4.2742-4.54180.18351860.151738043990100
4.5418-4.89220.17451820.149438544036100
4.8922-5.3840.20881840.163438764060100
5.384-6.16190.22592120.193338234035100
6.1619-7.75850.22362180.217238654083100
7.7585-49.56610.20341960.21240594255100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.23121.29560.27817.99061.21490.3613-0.27160.16330.0499-1.29390.23180.2405-0.33690.15020.06910.66990.0165-0.03790.45850.03390.353849.5805154.69535.4946
20.37590.91850.24377.52830.91710.6281-0.03060.0565-0.0293-0.0957-0.02610.06480.02550.06420.04620.39930.10910.02280.4142-0.03560.226543.9659118.03699.5428
31.47642.4311-0.69225.555-1.19621.0297-0.01870.08960.0855-0.25560.0524-0.0286-0.26320.2934-0.07580.5245-0.0471-0.04170.48610.01450.264658.7049176.395115.7794
40.81671.9796-0.67825.2701-1.26270.65580.0228-0.0149-0.0418-0.012-0.0453-0.20320.02690.15140.0230.35780.0813-0.10450.50050.07270.338350.8614126.133941.0137
51.28362.20680.57684.53711.22130.97830.1123-0.1386-0.02290.3719-0.0173-0.2032-0.16020.2861-0.04520.4487-0.0305-0.02810.5821-0.04330.32365.1275173.27436.2852
62.49353.40410.4795.4310.64150.56270.3026-0.26090.22090.3519-0.22760.4287-0.1274-0.0799-0.07520.29350.04080.05420.4306-0.0430.445521.4839144.564432.9232
72.33562.69170.81812.97521.00390.89570.19110.0178-0.42530.2215-0.0587-0.3090.08320.0901-0.13660.25560.0952-0.03450.40660.03630.563919.7739127.298226.412
80.91981.8051-0.01128.6044-0.51540.66230.1312-0.14140.43020.4649-0.09890.8154-0.48420.0333-0.03680.6444-0.01230.09730.4721-0.07860.445445.8191180.65232.7031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 79 )A8 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 314 )A80 - 314
3X-RAY DIFFRACTION3chain 'A' and (resid 315 through 500 )A315 - 500
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 342 )B8 - 342
5X-RAY DIFFRACTION5chain 'B' and (resid 343 through 501 )B343 - 501
6X-RAY DIFFRACTION6chain 'C' and (resid 8 through 146 )C8 - 146
7X-RAY DIFFRACTION7chain 'C' and (resid 147 through 314 )C147 - 314
8X-RAY DIFFRACTION8chain 'C' and (resid 315 through 500 )C315 - 500

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