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- PDB-4kpq: Structure and receptor binding specificity of the hemagglutinin H... -

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Basic information

Entry
Database: PDB / ID: 4kpq
TitleStructure and receptor binding specificity of the hemagglutinin H13 from avian influenza A virus H13N6
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / receptor binding
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
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / 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 / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsLu, X. / Qi, J. / Shi, Y. / Gao, G.
CitationJournal: J.Virol. / Year: 2013
Title: Structure and Receptor Binding Specificity of Hemagglutinin H13 from Avian Influenza A Virus H13N6
Authors: Lu, X. / Qi, J. / Shi, Y. / Wang, M. / Smith, D.F. / Heimburg-Molinaro, J. / Zhang, Y. / Paulson, J.C. / Xiao, H. / Gao, G.F.
History
DepositionMay 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 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
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,8367
Polymers169,6156
Non-polymers2211
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30510 Å2
ΔGint-159 kcal/mol
Surface area57400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.106, 77.061, 76.474
Angle α, β, γ (deg.)85.50, 82.55, 87.37
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Hemagglutinin /


Mass: 36691.195 Da / Num. of mol.: 3 / Fragment: HA1 chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Gull/Maryland/704/1977 H13N6 / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P13103
#2: Protein Hemagglutinin /


Mass: 19846.988 Da / Num. of mol.: 3 / Fragment: HA2 chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Gull/Maryland/704/1977 H13N6 / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P13103
#3: 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.: 1
Source method: isolated from a genetically manipulated 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.2M L-Proline, 0.1M HEPES, 10% PEG-3350, 0.01M Sodium Bromide, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 16, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 57001 / Num. obs: 57001 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.66 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F23

4f23


Resolution: 2.502→42.353 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7191 / SU ML: 0.42 / σ(F): 1.98 / Phase error: 33.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 2879 5.06 %random
Rwork0.2238 ---
all0.2255 56940 --
obs0.2255 56940 97.45 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.526 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso max: 220.29 Å2 / Biso mean: 77.2418 Å2 / Biso min: 31.24 Å2
Baniso -1Baniso -2Baniso -3
1--6.1482 Å2-9.7962 Å2-3.1784 Å2
2--21.5549 Å226.4261 Å2
3----15.4067 Å2
Refinement stepCycle: LAST / Resolution: 2.502→42.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11601 0 14 226 11841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311889
X-RAY DIFFRACTIONf_angle_d0.73616095
X-RAY DIFFRACTIONf_chiral_restr0.0511738
X-RAY DIFFRACTIONf_plane_restr0.0022101
X-RAY DIFFRACTIONf_dihedral_angle_d14.7674334
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5018-2.54280.42121100.37852299240988
2.5428-2.58670.43481440.37462562270698
2.5867-2.63370.42781440.35172607275198
2.6337-2.68440.41961280.33242610273898
2.6844-2.73910.37841420.30922553269598
2.7391-2.79870.30251320.29292602273498
2.7987-2.86380.31281140.28912649276398
2.8638-2.93540.3411270.27792602272998
2.9354-3.01470.31411420.28142589273198
3.0147-3.10340.35021380.27182594273299
3.1034-3.20350.2731400.26172607274798
3.2035-3.3180.27711780.24662592277099
3.318-3.45080.30541440.2372597274199
3.4508-3.60780.24261400.2282599273999
3.6078-3.79790.25311410.20362613275499
3.7979-4.03560.21151330.18992639277299
4.0356-4.34690.23191320.17832589272198
4.3469-4.78390.1851280.16412603273198
4.7839-5.47480.21041510.17112570272198
5.4748-6.89290.20771400.20722553269397
6.8929-42.35890.20521310.19772432256392
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)
13.91170.47191.071.02360.21952.0707-0.5157-1.24090.32710.15830.4664-0.0633-0.4712-0.18440.17160.6332-0.1229-0.01690.7168-0.10420.472144.6547-30.778535.7938
20.9837-0.3751.02920.4601-0.67321.4174-0.3369-0.33180.43620.21610.034-0.4109-0.4872-0.23880.12630.6495-0.1117-0.070.5277-0.05410.632428.5354-16.069617.8843
31.9457-0.28811.56560.5873-0.68551.5778-0.19940.19380.91870.4369-0.0876-0.1724-0.5187-0.20720.15850.85880.0401-0.01090.41450.0630.885311.45293.5782-6.4825
41.49540.1580.68540.5095-0.58952.1234-0.09140.95710.85610.3674-0.3823-0.2443-0.7170.56670.19630.8035-0.03890.02540.69480.26410.947611.57958.632-20.5556
52.1974-1.3937-0.56272.2308-0.03361.1895-0.41730.46371.51740.54510.34620.0655-0.6792-0.14480.46330.90090.0436-0.02880.66130.43941.13692.107316.1986-20.5736
62.2604-0.08490.83531.1842-0.86561.72930.05861.11820.37860.1183-0.3879-0.467-0.13240.27530.11150.65230.02730.09680.66990.2770.820610.26931.227-24.7442
70.84450.07310.77421.3659-1.4142.4462-0.38380.07140.4672-0.2433-0.0022-0.1534-0.8188-0.68830.04440.86220.18910.0010.91950.31420.9262-11.225210.7756-25.6474
82.7692-0.74780.211.8360.01812.61210.09860.44980.60390.5682-0.0278-0.2183-0.0809-0.51650.02450.66480.03520.13070.49790.17920.6866-4.35971.7756-20.2202
92.5963-0.5271.12181.3705-1.42421.68180.02850.66810.05440.1442-0.0833-0.18520.1412-0.12790.05160.52920.03420.10430.67380.22080.64316.2754-1.5066-23.1734
102.0067-0.02611.39431.0486-1.2382.2822-0.03240.59390.3496-0.065-0.2811-0.3033-0.32420.20630.16730.6573-0.0176-0.00610.45650.11350.711113.14960.1105-13.6965
111.6553-0.22260.20220.3009-0.69661.6091-0.2743-0.3790.47620.31190.061-0.3245-0.54140.17810.10280.5835-0.0789-0.04880.325-0.13410.567726.5541-13.615614.1112
121.6301-1.03620.70051.25380.04862.4542-0.2352-1.05490.36990.57870.0812-0.1464-0.39340.15930.04160.5018-0.2197-0.09330.543-0.02490.560244.8834-33.493433.4243
134.49480.04552.09051.70680.17454.2497-0.4605-0.80820.3270.8428-0.1979-0.4043-0.27580.54170.29610.6306-0.2386-0.1820.99620.05080.820359.0193-33.168138.7254
142.6625-0.76911.48860.7381-0.9441.94540.0527-0.17440.09050.115-0.1579-0.1952-0.04850.22560.08970.4345-0.10380.01610.4081-0.05090.419437.7241-30.875619.3204
154.08281.5673-1.76991.86241.79035.58040.07-0.2284-0.4706-0.1755-0.1138-1.02170.29311.24620.23620.59390.19820.03091.30810.20610.973967.4109-46.517933.1797
161.3203-0.70150.36311.7252-1.1253.3720.7568-0.6457-1.3188-0.4179-0.26250.39571.0863-0.6789-0.71040.9421-0.4323-0.30550.60860.48720.992127.2371-59.821630.2529
172.0993-0.71561.21240.8713-1.22362.41660.2245-0.6448-0.36390.12410.35110.38930.076-0.9877-0.3130.499-0.12330.02580.86010.18330.5984-9.0415-28.82655.3575
182.0619-0.77440.38410.46410.35741.60710.249-0.2869-0.2620.22470.22560.8487-0.1046-1.18310.18660.15790.20360.35451.44460.45150.7874-30.605-13.6393-4.3833
192.3278-0.58230.56822.1894-0.88421.90310.0419-0.11250.23770.1080.29450.2622-0.4889-0.7674-0.16360.53810.11620.19010.84610.18130.6443-20.0239-7.9367-9.4923
201.5474-0.36860.22691.0226-0.64911.38570.3015-0.9127-0.8584-0.01460.42410.40780.559-0.8578-0.1960.5397-0.2298-0.07990.75260.22060.63374.0814-40.433512.5747
210.71050.75170.07112.0804-1.34471.5970.3519-0.6767-1.12930.1910.24630.28540.8398-0.3840.820.7349-0.3503-0.15910.70760.50120.894629.5839-56.923931.6914
222.08171.9013-1.48365.33710.4256.6550.2394-0.5408-0.510.24440.11020.06420.8022-0.1060.41761.0635-0.159-0.14341.23680.72431.002431.7856-65.929648.3215
231.5889-0.93880.75683.1553-1.81512.7824-0.0772-0.6764-0.58840.50240.04960.0757-0.1689-0.165-0.17220.5433-0.1632-0.00520.63560.09280.545622.6102-42.689331.4459
241.8577-0.69861.0091.4837-1.68572.5450.4035-0.3268-0.3697-0.1317-0.2016-0.07480.4981-0.0399-0.20750.4676-0.1382-0.04930.2747-0.00720.395123.6844-42.697618.1539
251.0627-0.26810.39141.0347-0.2622.2018-0.2319-0.8154-0.24640.75210.0912-0.0770.3917-0.0889-0.21740.9291-0.2944-0.39721.33490.98830.553540.4691-54.806150.5566
262.116-1.53610.53823.7047-0.90121.43340.20860.66860.1986-0.4989-0.5984-0.72770.66051.08050.17850.91960.475-0.03490.9317-0.09120.56453.2751-51.1199.5341
270.7866-0.37340.64070.2866-0.52751.26440.48360.56340.0218-0.1154-0.4238-0.07491.07970.4847-0.14830.68660.2241-0.0030.671-0.09960.375134.2676-39.368-7.719
282.2429-1.45081.30741.2367-1.17842.17170.30570.5822-0.1909-0.3216-0.28360.08730.82320.0148-0.14920.68420.1248-0.01160.878-0.04020.420310.2433-29.6941-32.1544
292.3674-0.53920.85541.4691-0.34562.41610.2750.3565-0.1482-0.30080.00720.29120.4015-0.5064-0.2940.60620.0031-0.03520.8258-0.00240.4784-1.84-29.2329-28.9147
301.82240.03160.60051.83670.03712.42650.11940.89430.0854-0.74050.07930.27250.3443-0.48-0.22720.50310.0305-0.04641.150.1050.5139-7.28-21.907-39.1721
312.3431-0.35650.8811.9285-0.4914.39240.4081-0.02030.33880.375-0.02160.4923-0.5568-0.6493-0.31940.37880.04310.07151.070.14710.4009-15.2001-16.8944-27.9708
322.7386-0.94471.17611.11210.19362.34530.2110.40010.0787-0.21290.040.09190.1708-0.3598-0.20030.4418-0.0109-0.01750.80920.03030.4311-1.9609-23.0182-29.141
332.22890.8597-0.24553.1631-0.12244.43540.14911.1348-0.5123-0.7521-0.1148-0.56640.92820.1858-0.11440.69760.21830.00970.7932-0.30250.356524.6741-37.7242-22.9403
341.6465-0.73210.77990.7354-0.48362.03140.33790.31860.0444-0.1613-0.338-0.07820.83810.45-0.13310.59880.15060.00420.4663-0.09180.301433.1446-38.4241-4.5545
351.8035-1.87310.51473.2823-0.69014.43190.26110.1850.12960.0671-0.2234-0.8840.18361.2451-0.04180.81980.090.00480.5086-0.1360.56150.4641-46.631218.2641
365.44220.46811.19290.4785-0.24490.56330.32980.81-1.1478-0.8409-0.5263-0.12921.01220.4823-0.13021.14470.461-0.10821.1167-0.24720.75951.1092-55.96276.2372
373.90430.0017-1.3132.3950.48961.50350.67210.3284-1.0685-0.3505-0.2859-0.90970.46320.7042-0.08351.8070.5275-0.4710.9393-0.17961.076657.6643-64.697813.8831
382.5734-0.06773.72924.9901-1.26055.67320.25990.0947-0.5357-0.1301-0.32570.2360.54950.6289-0.05831.62190.4115-0.43941.1819-0.02620.787653.1541-63.25279.7728
391.9506-0.60770.85271.1272-0.19221.50790.59460.1066-0.464-0.3053-0.11410.35850.7860.062-0.07460.67430.0497-0.05660.3515-0.17490.369124.7811-42.1242-1.5628
402.4136-0.72070.82930.8567-0.53391.51560.136-0.3402-0.39790.1280.13990.18970.31550.0752-0.09630.62070.0296-0.02380.4321-0.09960.409634.6154-40.679.73
411.818-1.2730.53891.0838-0.90161.60580.65650.2094-1.1577-0.52020.01720.20191.28350.954-0.18491.42790.6024-0.28371.0966-0.00711.033956.0382-66.140620.6907
421.4045-0.21651.06180.9086-0.87322.43110.335-0.4118-0.7931-0.0085-0.1365-0.32850.93130.7238-0.01431.63430.1743-0.28281.19430.80931.996253.0943-72.066628.9476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 4:23)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 24:51)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 52:109)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 110:137)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 138:163)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 164:184)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 185:201)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 202:228)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 229:247)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 248:271)
11X-RAY DIFFRACTION11CHAIN A AND (RESSEQ 272:327)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 2:21)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 22:31)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 32:153)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 154:166)
16X-RAY DIFFRACTION16CHAIN C AND (RESSEQ 4:23)
17X-RAY DIFFRACTION17CHAIN C AND (RESSEQ 24:120)
18X-RAY DIFFRACTION18CHAIN C AND (RESSEQ 121:150)
19X-RAY DIFFRACTION19CHAIN C AND (RESSEQ 151:265)
20X-RAY DIFFRACTION20CHAIN C AND (RESSEQ 266:327)
21X-RAY DIFFRACTION21CHAIN D AND (RESSEQ 2:25)
22X-RAY DIFFRACTION22CHAIN D AND (RESSEQ 26:33)
23X-RAY DIFFRACTION23CHAIN D AND (RESSEQ 34:57)
24X-RAY DIFFRACTION24CHAIN D AND (RESSEQ 58:145)
25X-RAY DIFFRACTION25CHAIN D AND (RESSEQ 146:166)
26X-RAY DIFFRACTION26CHAIN E AND (RESSEQ 4:23)
27X-RAY DIFFRACTION27CHAIN E AND (RESSEQ 24:51)
28X-RAY DIFFRACTION28CHAIN E AND (RESSEQ 52:97)
29X-RAY DIFFRACTION29CHAIN E AND (RESSEQ 98:130)
30X-RAY DIFFRACTION30CHAIN E AND (RESSEQ 131:195)
31X-RAY DIFFRACTION31CHAIN E AND (RESSEQ 196:214)
32X-RAY DIFFRACTION32CHAIN E AND (RESSEQ 215:271)
33X-RAY DIFFRACTION33CHAIN E AND (RESSEQ 272:289)
34X-RAY DIFFRACTION34CHAIN E AND (RESSEQ 290:327)
35X-RAY DIFFRACTION35CHAIN F AND (RESSEQ 2:11)
36X-RAY DIFFRACTION36CHAIN F AND (RESSEQ 12:21)
37X-RAY DIFFRACTION37CHAIN F AND (RESSEQ 22:31)
38X-RAY DIFFRACTION38CHAIN F AND (RESSEQ 32:37)
39X-RAY DIFFRACTION39CHAIN F AND (RESSEQ 38:74)
40X-RAY DIFFRACTION40CHAIN F AND (RESSEQ 75:132)
41X-RAY DIFFRACTION41CHAIN F AND (RESSEQ 133:154)
42X-RAY DIFFRACTION42CHAIN F AND (RESSEQ 155:166)

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