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- PDB-8gv6: Crystal structure of PN-SIA28 in complex with influenza hemagglut... -

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Basic information

Entry
Database: PDB / ID: 8gv6
TitleCrystal structure of PN-SIA28 in complex with influenza hemagglutinin H14 (A/long-tailed duck/Wisconsin/10OS3912/2010)
Components
  • (Hemagglutinin H14- ...) x 2
  • PN-SIA28 heavy chain
  • PN-SIA28 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Influenza / hemagglutinin / antibody / broadly neutralizing / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like ...Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsChen, Y. / Song, H. / Qi, J. / Gao, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for a human broadly neutralizing influenza A hemagglutinin stem-specific antibody including H17/18 subtypes.
Authors: Chen, Y. / Wang, F. / Yin, L. / Jiang, H. / Lu, X. / Bi, Y. / Zhang, W. / Shi, Y. / Burioni, R. / Tong, Z. / Song, H. / Qi, J. / Gao, G.F.
History
DepositionSep 14, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin H14-HA1
B: Hemagglutinin H14-HA2
C: Hemagglutinin H14-HA1
D: Hemagglutinin H14-HA2
E: Hemagglutinin H14-HA1
F: Hemagglutinin H14-HA2
G: PN-SIA28 heavy chain
H: PN-SIA28 light chain
I: PN-SIA28 heavy chain
J: PN-SIA28 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,53715
Polymers219,61810
Non-polymers1,9195
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.662, 120.990, 129.759
Angle α, β, γ (deg.)90.000, 107.730, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Hemagglutinin H14- ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin H14-HA1


Mass: 35512.953 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/long-tailed duck/Wisconsin/10OS3912/2010(H14N6))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G5DSS3
#2: Protein Hemagglutinin H14-HA2


Mass: 20949.082 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/long-tailed duck/Wisconsin/10OS3912/2010(H14N6))
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G5DSS3

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Antibody , 2 types, 4 molecules GIHJ

#3: Antibody PN-SIA28 heavy chain


Mass: 13588.259 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody PN-SIA28 light chain


Mass: 11527.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Sugars , 2 types, 5 molecules

#5: 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 genetically manipulated 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
#6: 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.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

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Details

Has ligand of interestY
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: 3.12 Å3/Da / Density % sol: 60.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris, 5% w/v PGA-LM, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 36855 / % possible obs: 87 % / Redundancy: 5.4 % / Biso Wilson estimate: 61.99 Å2 / Rmerge(I) obs: 0.3 / Net I/σ(I): 5.58
Reflection shellResolution: 3.4→3.52 Å / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3591

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX1.20_4459refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJS

5gjs


Resolution: 3.4→49.72 Å / SU ML: 0.4499 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.886
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2614 1615 4.95 %
Rwork0.2212 31022 -
obs0.2232 32637 86.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.55 Å2
Refinement stepCycle: LAST / Resolution: 3.4→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15000 0 126 0 15126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315436
X-RAY DIFFRACTIONf_angle_d0.585420929
X-RAY DIFFRACTIONf_chiral_restr0.0532328
X-RAY DIFFRACTIONf_plane_restr0.00422729
X-RAY DIFFRACTIONf_dihedral_angle_d14.26775628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.490.38610.32831047X-RAY DIFFRACTION35.82
3.49-3.60.42081040.29981628X-RAY DIFFRACTION56.07
3.6-3.730.29761290.27322152X-RAY DIFFRACTION73.58
3.73-3.880.33771470.27672571X-RAY DIFFRACTION87.06
3.88-4.060.30361320.26322837X-RAY DIFFRACTION95.16
4.06-4.270.29981340.23392907X-RAY DIFFRACTION97.97
4.27-4.540.25041520.20612942X-RAY DIFFRACTION98.72
4.54-4.890.24691580.19452958X-RAY DIFFRACTION99.3
4.89-5.380.22951560.18832970X-RAY DIFFRACTION99.74
5.38-6.160.26171490.20452970X-RAY DIFFRACTION99.65
6.16-7.750.2181460.20782993X-RAY DIFFRACTION99.71
7.76-49.720.18551470.18973047X-RAY DIFFRACTION99.41
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)
11.21026450798-0.134576861795-0.6277536099520.4161643907150.03723900559870.930634087595-0.00621896692019-0.09378511965990.100703120009-0.06205464736840.0404964482364-0.119366235260.1802443584560.281018928401-0.06491112697220.2660563883670.0439468473613-0.02926667921910.241101036806-0.01209042270010.3001774410694.933-1.80919.49
20.6811574824320.0322835346675-0.3491367787820.750287635141-0.1940978929661.786949768050.0512704624869-0.4485845490410.1029858565040.237017873060.0562818833640.09918564668430.03130716388630.140236571094-0.02161383649050.3228941902750.0463497440525-0.02154311912310.371169932091-0.04460448029190.256826672608-28.779-0.00858.107
30.852812132829-0.301457761107-0.5667058321390.422064847883-0.235306292111.161690874880.01726714847770.204323341386-0.145563546921-0.146226583277-0.17850524989-0.02686812273570.173721756425-0.0217728475198-0.002428451841660.412133319858-0.0497301339576-0.08026596798090.253709641561-0.06541269251570.274400889015-19.479-14.412.531
41.145971978270.228243931402-0.7268282984090.74682156492-0.415293821220.820010234-0.161417243-0.156273375392-0.08985182715720.1015374268960.04675437540060.1577071703770.1733505803580.0458900569541-0.04171667078310.2893994811890.004016386343280.03669003033810.320766583888-0.02823600517040.310007153472-42.798-11.96448.324
50.7246566947360.0174304393941-0.4381460185620.387757934211-0.2945282775691.269222818740.2121837925410.2461453322090.222008989274-0.04433025422-0.0557162321905-0.00226850395737-0.170302849616-0.000108944833193-0.098417720030.355636998979-0.02177226595420.019368341620.225481113065-0.001676752308290.35229556153-16.80917.355.449
61.26427582938-0.441908868294-0.6392328928790.3470547267870.2735727951741.3970915916-0.0396032311899-0.0451239563027-0.0122908126030.0935713748454-0.01437377776110.151340588813-0.309486375832-0.336188887833-0.1420767414230.3616833528190.002244081223510.03011500132630.284118797612-0.03293269820310.396002494279-44.6348.8947.665
72.113779462530.3847127098690.09147110995871.331262956790.1934530619531.411701341290.4065781178260.212578669419-0.4453335251710.0848640533051-0.1495743746970.1868453837060.421986947983-0.393632774407-0.0454605387760.413740407382-0.0933332273651-0.03246220851370.4827741514710.0470822047210.448474586607-65.386-32.12239.432
80.5819013162520.2229720495930.1681372893630.584852089067-0.6910333128681.81894941310.1021417286750.9372008247010.3128159404590.00638382745218-0.283268307404-0.229139490671-0.0910004459814-0.145339872802-0.06897627995260.4883471364340.1233238343970.02058699018650.8936071993890.1686243087340.427188432034-58.034-18.24924.133
90.249908621675-0.0283915000085-0.23867227792.1218473046-0.4352754715980.3258912387660.0826163953505-0.4321950027681.40645534619-0.1986466647730.0874183556204-0.0112008659737-0.3344770510220.1515729948430.3950189261680.578172403298-0.02280065727040.3098168624890.532224342263-0.2637119344921.58264175464-50.98539.57548.403
101.024262273580.475945616584-0.4224535028260.565792237429-0.1617302042360.2901421711260.359711303664-0.05281781945370.8702832787-0.287054309930.056395875822-0.199377184928-0.5315381265820.727142850029-0.05940041595930.645960252639-0.1696416238550.213453301360.957097113085-0.2424492610891.47593679083-30.70433.32142.926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 8:325 )A8 - 325
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:172 )B1 - 172
3X-RAY DIFFRACTION3( CHAIN C AND RESID 8:325 )C8 - 325
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:172 )D1 - 172
5X-RAY DIFFRACTION5( CHAIN E AND ( RESID 8:325 OR RESID 501:501 ) )E8 - 325
6X-RAY DIFFRACTION5( CHAIN E AND ( RESID 8:325 OR RESID 501:501 ) )E501
7X-RAY DIFFRACTION6( CHAIN F AND RESID 1:172 )F1 - 172
8X-RAY DIFFRACTION7( CHAIN G AND RESID 31:154 )G31 - 154
9X-RAY DIFFRACTION8( CHAIN H AND RESID 43:149 )H43 - 149
10X-RAY DIFFRACTION9( CHAIN I AND RESID 31:154 )I31 - 154
11X-RAY DIFFRACTION10( CHAIN J AND RESID 43:149 )J43 - 149

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