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- PDB-3qqi: Crystal structure of the HA1 receptor binding domain of H2 hemagg... -

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Basic information

Entry
Database: PDB / ID: 3qqi
TitleCrystal structure of the HA1 receptor binding domain of H2 hemagglutinin
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / viral envelope protein / hemagglutinin / viral fusion protein
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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsXu, R. / Wilson, I.A.
CitationJournal: J.Virol. / Year: 2011
Title: Structural Characterization of an Early Fusion Intermediate of Influenza Virus Hemagglutinin.
Authors: Xu, R. / Wilson, I.A.
History
DepositionFeb 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0586
Polymers49,1392
Non-polymers9194
Water11,097616
1
A: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0293
Polymers24,5701
Non-polymers4602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0293
Polymers24,5701
Non-polymers4602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.629, 62.318, 66.034
Angle α, β, γ (deg.)64.250, 80.040, 72.120
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Hemagglutinin /


Mass: 24569.625 Da / Num. of mol.: 2 / Fragment: HA1 receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Japan/305/1957 H2N2 / Gene: HA, hemagglutinin / Plasmid: pFASTbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: C7S226
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 1.25 Sodium Citrate, 0.1M HEPES, pH 8.1, vapor diffusion, sitting drop, temperature 295.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97958 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2009
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionRedundancy: 1.9 % / Av σ(I) over netI: 11.5 / Number: 112600 / Rmerge(I) obs: 0.053 / Χ2: 1.05 / D res high: 1.65 Å / D res low: 50 Å / Num. obs: 60290 / % possible obs: 94.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.555096.910.0371.0411.9
2.823.5597.710.051.0061.9
2.462.8297.310.0591.0381.9
2.242.4696.910.0690.9761.9
2.082.2496.510.0831.0361.9
1.962.0896.610.0921.0951.9
1.861.9696.210.1231.0511.9
1.781.8694.710.1571.0711.8
1.711.7891.510.2071.0861.8
1.651.7183.810.2441.0921.6
ReflectionResolution: 1.65→50 Å / Num. obs: 60290 / % possible obs: 94.8 % / Redundancy: 1.9 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.053 / Χ2: 1.046 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.65-1.711.60.24453121.09283.8
1.71-1.781.80.20758581.08691.5
1.78-1.861.80.15759991.07194.7
1.86-1.961.90.12361481.05196.2
1.96-2.081.90.09261271.09596.6
2.08-2.241.90.08361251.03696.5
2.24-2.461.90.06961500.97696.9
2.46-2.821.90.05961991.03897.3
2.82-3.551.90.0562141.00697.7
3.55-501.90.03761581.04196.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_FRF
Highest resolutionLowest resolution
Rotation2.5 Å36.72 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→36.72 Å / Cor.coef. Fo:Fc: 0.9439 / Cor.coef. Fo:Fc free: 0.9261 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 3056 5.08 %RANDOM
Rwork0.1993 ---
obs0.201 60214 --
Displacement parametersBiso max: 110.61 Å2 / Biso mean: 26.9027 Å2 / Biso min: 10.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.251 Å21.1955 Å20.0121 Å2
2--0.3335 Å21.9371 Å2
3----1.5845 Å2
Refine analyzeLuzzati coordinate error obs: 0.204 Å
Refinement stepCycle: LAST / Resolution: 1.65→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 58 616 4126
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d12612
X-RAY DIFFRACTIONt_trig_c_planes882
X-RAY DIFFRACTIONt_gen_planes5285
X-RAY DIFFRACTIONt_it363420
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion4635
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact45574
X-RAY DIFFRACTIONt_bond_d363420.011
X-RAY DIFFRACTIONt_angle_deg494321.12
X-RAY DIFFRACTIONt_omega_torsion3.96
X-RAY DIFFRACTIONt_other_torsion16.96
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2504 193 4.94 %
Rwork0.2303 3713 -
all0.2313 3906 -
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)
11.1522-0.4629-0.12960.8120.28480.43960.02330.01120.0191-0.0303-0.0413-0.02860.02810.0170.0179-0.0017-0.00860.018-0.0040.00420.01215.3139-25.3004-6.0786
21.09820.3288-0.05570.82080.15640.33870.0338-0.0127-0.01560.0388-0.0377-0.0293-0.0250.01380.0039-0.0124-0.01060.0084-0.01740.0036-0.000515.4329-57.058119.5309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|48 - A|266 }A48 - 266
2X-RAY DIFFRACTION2{ B|48 - B|266 }B48 - 266

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