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- PDB-4s1x: Crystal structure of HA2-Del-L2seM, Central Coiled-Coil from Infl... -

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Basic information

Entry
Database: PDB / ID: 4s1x
TitleCrystal structure of HA2-Del-L2seM, Central Coiled-Coil from Influenza Hemagglutinin HA2 without Heptad Repeat Stutter
ComponentsTruncated hemagglutinin
KeywordsVIRAL PROTEIN / Marburg Virus / GP2 Ectodomain / Post-Fusion Conformation
Function / homologyHaemagglutinin, influenzavirus B / Haemagglutinin / Haemagglutinin, influenzavirus A/B / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / Truncated hemagglutinin / Truncated hemagglutinin
Function and homology information
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMalashkevich, V.N. / Higgins, C.D. / Lai, J.R. / Almo, S.C.
CitationJournal: Biopolymers / Year: 2015
Title: A switch from parallel to antiparallel strand orientation in a coiled-coil X-ray structure via two core hydrophobic mutations.
Authors: Malashkevich, V.N. / Higgins, C.D. / Almo, S.C. / Lai, J.R.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Truncated hemagglutinin
B: Truncated hemagglutinin
C: Truncated hemagglutinin
D: Truncated hemagglutinin
E: Truncated hemagglutinin
F: Truncated hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3767
Polymers28,2846
Non-polymers921
Water97354
1
A: Truncated hemagglutinin
B: Truncated hemagglutinin
C: Truncated hemagglutinin


Theoretical massNumber of molelcules
Total (without water)14,1423
Polymers14,1423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-40 kcal/mol
Surface area7330 Å2
MethodPISA
2
D: Truncated hemagglutinin
E: Truncated hemagglutinin
F: Truncated hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2344
Polymers14,1423
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-37 kcal/mol
Surface area7170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.450, 98.523, 34.553
Angle α, β, γ (deg.)90.000, 89.960, 90.000
Int Tables number4
Space group name H-MP1211
Detailstrimer or tetramer

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Components

#1: Protein/peptide
Truncated hemagglutinin


Mass: 4713.993 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: peptide synthesis / Source: (synth.) unidentified influenza virus / References: UniProt: A8TXJ0, UniProt: A8TXX2*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG 4000, 5% 2-propanol, 0.1 M HEPES:NaOH, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.374
11-h,-k,l20.141
11L, -K, H30.098
11-L, K, H40.388
ReflectionResolution: 1.9→50 Å / Num. obs: 18167 / % possible obs: 99.6 % / Redundancy: 5 % / Rmerge(I) obs: 0.077 / Χ2: 1.046 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.935.20.7419371.166199.9
1.93-1.975.30.5618631.1011100
1.97-2.015.20.4778991.1721100
2.01-2.055.30.3439431.1551100
2.05-2.095.30.2948831.1411100
2.09-2.145.30.2439421.0651100
2.14-2.195.30.2138851.0161100
2.19-2.255.30.198851.0911100
2.25-2.325.20.159511.0191100
2.32-2.395.20.1428710.9391100
2.39-2.485.20.1249350.9311100
2.48-2.585.20.1158900.984199.9
2.58-2.75.10.10592011100
2.7-2.8450.0969261.0231100
2.84-3.024.80.0848760.932199.8
3.02-3.254.60.0759341.046199.8
3.25-3.584.40.0639030.988199.8
3.58-4.094.50.0579131.142199.8
4.09-5.164.40.0539140.969198.9
5.16-5040.0538970.982194.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→28.29 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.937 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 871 4.8 %RANDOM
Rwork0.2078 ---
obs0.2095 18235 98.69 %-
all-18235 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.46 Å2 / Biso mean: 41.059 Å2 / Biso min: 25.83 Å2
Baniso -1Baniso -2Baniso -3
1-27.5 Å20 Å225.47 Å2
2---46.54 Å2-0 Å2
3---19.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 6 54 1708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191683
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.9592218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7735186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44725.534103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98315337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4161511
X-RAY DIFFRACTIONr_chiral_restr0.080.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021251
X-RAY DIFFRACTIONr_mcbond_it1.9575.454768
X-RAY DIFFRACTIONr_mcangle_it2.88673.466940
X-RAY DIFFRACTIONr_scbond_it3.3166.351915
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 66 -
Rwork0.214 1156 -
all-1222 -
obs--92.16 %
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)
10.6674-1.40540.54073.2122-0.94850.6829-0.05630.03280.05470.1236-0.0277-0.1454-0.0680.04250.0840.0094-0.0031-0.01010.02370.01470.07752.469611.6098-12.2795
20.0588-0.18960.12464.859-1.5590.65510.01540.0376-0.00690.0327-0.051-0.0006-0.00020.07710.03560.0090.0069-0.00170.02960.00120.0369-4.712712.5235-18.9204
30.81141.69010.12143.63220.25090.02290.01370.03-0.07790.0785-0.023-0.2276-0.00660.00930.00930.042-0.0505-0.05840.07410.06010.10575.81326.9384-17.8399
40.3397-0.6664-0.18413.34470.89150.26090.06990.05570.07030.013-0.0747-0.09070.0156-0.03880.00480.0330.0020.03410.0243-0.00640.0528-12.436436.4155-2.4359
50.5953-1.6679-0.06745.40120.32490.06240.03510.04480.00870.0344-0.0720.01920.0296-0.01990.0370.02760.0050.01890.0347-0.01050.0411-18.945537.10674.7547
60.74520.2666-0.04611.8557-0.43750.1336-0.05230.11520.0119-0.09380.1173-0.00940.0296-0.0444-0.0650.06410.01830.00210.04950.03850.0996-17.908351.5442-5.8756
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 83
2X-RAY DIFFRACTION2B43 - 83
3X-RAY DIFFRACTION3C45 - 70
4X-RAY DIFFRACTION4D42 - 83
5X-RAY DIFFRACTION5E43 - 101
6X-RAY DIFFRACTION6F45 - 70

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