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- PDB-6d8w: Crystal structure of InvbI.18715.a.KN11: Influenza hemagglutinin ... -

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Basic information

Entry
Database: PDB / ID: 6d8w
TitleCrystal structure of InvbI.18715.a.KN11: Influenza hemagglutinin from strain A/Jiangsu/ALSI/2011
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / Inflenza hemagglutinin / Structural Genomics / STRIVE / SSGCID / 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
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
FORMIC ACID / OXAMIC ACID / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: 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
DepositionApr 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2May 24, 2023Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,10920
Polymers336,2446
Non-polymers1,86414
Water16,376909
1
A: Hemagglutinin
D: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,23111
Polymers168,1223
Non-polymers1,1098
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-31 kcal/mol
Surface area57150 Å2
MethodPISA
2
B: Hemagglutinin
C: Hemagglutinin
E: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,8789
Polymers168,1223
Non-polymers7566
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-42 kcal/mol
Surface area57900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.300, 113.330, 130.120
Angle α, β, γ (deg.)110.160, 90.850, 90.280
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 7 and (name N or name...
21(chain B and ((resid 7 and (name N or name...
31(chain C and ((resid 7 and (name N or name...
41(chain D and (resid 7 through 12 or (resid 13...
51(chain E and ((resid 7 and (name N or name...
61(chain F and ((resid 7 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 7 and (name N or name...A7
121(chain A and ((resid 7 and (name N or name...A4 - 600
131(chain A and ((resid 7 and (name N or name...A4 - 600
141(chain A and ((resid 7 and (name N or name...A4 - 600
151(chain A and ((resid 7 and (name N or name...A4 - 600
211(chain B and ((resid 7 and (name N or name...B7
221(chain B and ((resid 7 and (name N or name...B1 - 600
231(chain B and ((resid 7 and (name N or name...B1 - 600
241(chain B and ((resid 7 and (name N or name...B1 - 600
251(chain B and ((resid 7 and (name N or name...B1 - 600
311(chain C and ((resid 7 and (name N or name...C7
321(chain C and ((resid 7 and (name N or name...C2 - 486
331(chain C and ((resid 7 and (name N or name...C2 - 486
341(chain C and ((resid 7 and (name N or name...C2 - 486
351(chain C and ((resid 7 and (name N or name...C2 - 486
411(chain D and (resid 7 through 12 or (resid 13...D7 - 12
421(chain D and (resid 7 through 12 or (resid 13...D13 - 15
431(chain D and (resid 7 through 12 or (resid 13...D7 - 486
441(chain D and (resid 7 through 12 or (resid 13...D7 - 486
451(chain D and (resid 7 through 12 or (resid 13...D7 - 486
461(chain D and (resid 7 through 12 or (resid 13...D7 - 486
511(chain E and ((resid 7 and (name N or name...E7
521(chain E and ((resid 7 and (name N or name...E3 - 491
531(chain E and ((resid 7 and (name N or name...E3 - 491
541(chain E and ((resid 7 and (name N or name...E3 - 491
551(chain E and ((resid 7 and (name N or name...E3 - 491
611(chain F and ((resid 7 and (name N or name...F7
621(chain F and ((resid 7 and (name N or name...F3 - 601
631(chain F and ((resid 7 and (name N or name...F3 - 601
641(chain F and ((resid 7 and (name N or name...F3 - 601
651(chain F and ((resid 7 and (name N or name...F3 - 601

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Components

#1: Protein
Hemagglutinin


Mass: 56040.707 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G0Z9B7
#2: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / 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
#3: Chemical
ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 909 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: SEC purified InvbI.18715.a.KN11.PD38282 at 10.18mg/ml (in 25mM MES pH 6.5, 150mM NaCl) was crystallized by sitting drop vapor diffusion at 14C with an equal volume (0.2:0.2uL) of protein: ...Details: SEC purified InvbI.18715.a.KN11.PD38282 at 10.18mg/ml (in 25mM MES pH 6.5, 150mM NaCl) was crystallized by sitting drop vapor diffusion at 14C with an equal volume (0.2:0.2uL) of protein:mother liquor (20mM each sodium formate, ammonium acetate, sodium citrate, sodium potassium tartrate, and sodium oxamate, 0.1M HEPES pH6.8, 17.2% PEG 500 MME, 8.6% PEG20k), then directly frozen for data collection. Crystal ID 297353a3 data set sht6-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→43.292 Å / Num. obs: 146567 / % possible obs: 97.4 % / Redundancy: 2.641 % / Biso Wilson estimate: 40.16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.079 / Χ2: 1.024 / Net I/σ(I): 11.91 / Num. measured all: 387137 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.412.6610.5492.13108580.7410.69196.9
2.41-2.482.6640.4582.6104510.8170.57597
2.48-2.552.660.42.96102570.8570.50297.1
2.55-2.632.6650.3413.4999280.8930.42897
2.63-2.712.660.2674.3596630.9360.33697.2
2.71-2.812.6620.2035.6394190.9620.25497.4
2.81-2.912.6580.1597.0589850.9720.297.2
2.91-3.032.6540.1258.6386350.980.15797.3
3.03-3.172.6410.09111.2183240.9890.11497.5
3.17-3.322.6410.07413.5780130.9920.09397.5
3.32-3.52.630.05616.4275920.9940.07197.6
3.5-3.722.620.04719.0771760.9950.0697.8
3.72-3.972.6190.0421.1767580.9960.05197.9
3.97-4.292.6150.03523.6663080.9970.04598.1
4.29-4.72.6080.03225.6858120.9970.0498.1
4.7-5.252.610.03225.8352630.9980.0498.2
5.25-6.072.6110.03325.3346320.9970.04298.2
6.07-7.432.60.03225.7539090.9970.04198.2
7.43-10.512.5940.02629.5530010.9980.03397.7
10.51-43.2922.5630.02631.115830.9970.03393.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vli,2wr0

5vli

2wr0


Resolution: 2.35→43.292 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 2041 1.39 %
Rwork0.1792 144475 -
obs0.1798 146516 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.11 Å2 / Biso mean: 60.4921 Å2 / Biso min: 16.76 Å2
Refinement stepCycle: final / Resolution: 2.35→43.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21388 0 121 916 22425
Biso mean--86.5 48.47 -
Num. residues----2829
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A10879X-RAY DIFFRACTION10.89TORSIONAL
12B10879X-RAY DIFFRACTION10.89TORSIONAL
13C10879X-RAY DIFFRACTION10.89TORSIONAL
14D10879X-RAY DIFFRACTION10.89TORSIONAL
15E10879X-RAY DIFFRACTION10.89TORSIONAL
16F10879X-RAY DIFFRACTION10.89TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.40460.30991370.25589613975097
2.4046-2.46480.32831300.23189527965797
2.4648-2.53140.28371170.23129610972797
2.5314-2.60590.29431410.22329608974997
2.6059-2.690.28991330.22419677981097
2.69-2.78610.29491250.21079586971197
2.7861-2.89760.23841450.219579972497
2.8976-3.02950.30061320.20869622975497
3.0295-3.18910.24141380.1989639977798
3.1891-3.38890.22131660.19079632979898
3.3889-3.65040.221440.17379636978098
3.6504-4.01750.19981220.15599701982398
4.0175-4.59830.17441420.1389676981898
4.5983-5.79120.18611340.14489709984398
5.7912-43.29950.19941350.17429660979597
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)
10.6381-0.0352-0.18750.03030.06644.86210.00480.3391-0.0039-0.3967-0.15230.2535-0.3746-0.53020.12520.57140.0542-0.11460.46460.04610.3940.9244-51.2472-59.3394
21.70090.1781-0.27283.13440.78892.312-0.0061-0.0977-0.12360.28050.09490.14440.2589-0.2074-0.09590.2134-0.03940.01290.22120.0550.29746.9327-59.3923-24.6597
30.47820.3565-0.00230.2660.59041.07030.06830.3824-0.0108-0.36870.03320.1782-0.1341-0.4859-0.14530.80590.0397-0.14680.72090.04310.37723.1741-54.5736-78.1657
40.66630.48870.92450.61450.08362.0143-0.03650.4277-0.1246-0.65180.2920.1535-0.2548-0.2547-0.13070.91070.0331-0.18170.8621-0.05150.35498.6884-57.0726-94.9511
51.06910.21170.51880.27960.04573.1149-0.17010.32710.2672-0.1276-0.0640.2263-0.4038-0.32760.20410.33140.0656-0.03370.36680.05840.4035-34.51854.4223-57.6972
62.72090.15981.17581.3997-0.29032.29820.0857-0.48530.14650.1795-0.0483-0.0171-0.0884-0.2815-0.04750.17380.00080.06210.2662-0.03920.2798-26.4254-4.2895-27.0352
71.81280.24761.13690.49230.30612.7146-0.1490.89860.1044-0.44020.11060.2436-0.2065-0.04890.05590.6067-0.0781-0.13620.88590.12660.3747-29.71122.5003-85.8289
81.187-0.23390.89490.9852-0.59622.87340.09440.339-0.2567-0.26120.0404-0.02320.3180.1698-0.14620.24240.01040.03850.3008-0.0610.3620.7872-19.6802-54.1559
92.54410.8676-0.73733.0245-0.68962.5760.1259-0.1829-0.00630.3812-0.0159-0.0211-0.15250.0908-0.08540.18780.02710.0030.15880.00280.28927.5396-12.7849-28.0645
101.55120.11610.35090.12350.28331.8153-0.06121.0333-0.2081-0.44090.14350.026-0.04930.2936-0.06890.7534-0.1103-0.02630.9587-0.09570.2778-9.918-12.5909-84.6671
110.6213-0.38731.83760.13950.21544.97820.43360.3076-0.3075-0.40320.04720.06751.440.2342-0.39450.9633-0.0477-0.16520.4916-0.04920.557728.5144-79.2365-62.2069
122.44510.25720.26772.253-0.07143.09910.2101-0.005-0.2160.02850.0623-0.28030.61720.3551-0.19390.32840.0931-0.0680.1801-0.02230.462638.5767-72.3759-30.7465
130.8628-0.00990.5613-0.10860.57462.89430.23810.5289-0.1984-0.24940.1223-0.0570.51930.5596-0.30661.04110.0531-0.1080.7106-0.1030.398323.1262-70.7356-91.0634
140.09630.60320.48220.98850.63062.9215-0.06550.41140.0609-0.51170.0996-0.1987-0.20970.2755-0.02380.44930.10330.08630.5523-0.0060.405438.4699-40.6628-64.1968
152.560.24660.0732.7915-0.47212.53060.117-0.1841-0.08070.2852-0.1292-0.2409-0.0580.07510.01710.1949-0.0086-0.01770.1526-0.00320.347833.7323-37.1394-31.3132
160.19320.22130.191.4045-0.35911.926-0.2130.39110.0949-0.79530.1061-0.1351-0.12690.04340.04620.8515-0.01990.03270.70210.00440.323629.786-48.9167-84.1393
170.3148-0.1092-0.28690.22191.05755.1315-0.12280.79690.3969-2.26730.31330.33770.1403-0.0877-0.02271.896-0.3115-0.09851.19660.20440.702226.0668-42.6892-120.7548
180.81351.09130.96421.10961.10065.0223-0.52430.71120.3238-0.73740.3061-0.1826-0.87820.51780.13560.7149-0.17480.02230.62840.11340.3842.655119.2386-61.2872
192.96150.76430.41093.7376-0.16152.68260.005-0.32830.22070.391-0.1484-0.0074-0.32720.10930.12310.2975-0.036-0.02550.1877-0.00120.3939-1.010719.8445-27.9011
200.1720.69710.48161.9906-0.10620.824-0.57210.58960.1687-0.95080.47720.1103-0.8570.49690.16521.0308-0.2871-0.07510.9520.1650.3149-7.441112.6035-82.6624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 3 through 99 )E3 - 99
2X-RAY DIFFRACTION2chain 'E' and (resid 100 through 269 )E100 - 269
3X-RAY DIFFRACTION3chain 'E' and (resid 270 through 403 )E270 - 403
4X-RAY DIFFRACTION4chain 'E' and (resid 404 through 491 )E404 - 491
5X-RAY DIFFRACTION5chain 'F' and (resid 3 through 99 )F3 - 99
6X-RAY DIFFRACTION6chain 'F' and (resid 100 through 288 )F100 - 288
7X-RAY DIFFRACTION7chain 'F' and (resid 289 through 486 )F289 - 486
8X-RAY DIFFRACTION8chain 'A' and (resid 4 through 138 )A4 - 138
9X-RAY DIFFRACTION9chain 'A' and (resid 139 through 266 )A139 - 266
10X-RAY DIFFRACTION10chain 'A' and (resid 267 through 484 )A267 - 484
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 99 )B1 - 99
12X-RAY DIFFRACTION12chain 'B' and (resid 100 through 288 )B100 - 288
13X-RAY DIFFRACTION13chain 'B' and (resid 289 through 496 )B289 - 496
14X-RAY DIFFRACTION14chain 'C' and (resid 2 through 99 )C2 - 99
15X-RAY DIFFRACTION15chain 'C' and (resid 100 through 288 )C100 - 288
16X-RAY DIFFRACTION16chain 'C' and (resid 289 through 452 )C289 - 452
17X-RAY DIFFRACTION17chain 'C' and (resid 453 through 486 )C453 - 486
18X-RAY DIFFRACTION18chain 'D' and (resid 7 through 99 )D7 - 99
19X-RAY DIFFRACTION19chain 'D' and (resid 100 through 269 )D100 - 269
20X-RAY DIFFRACTION20chain 'D' and (resid 270 through 486 )D270 - 486

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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