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- PDB-7khu: Crystal structure of the carbohydrate-binding domain VP8* of huma... -

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Basic information

Entry
Database: PDB / ID: 7khu
TitleCrystal structure of the carbohydrate-binding domain VP8* of human P[4] rotavirus strain BM5265 in complex with LNDFH I
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / Rotavirus / host receptor interaction / VIRUS
Function / homology
Function and homology information


host cytoskeleton / viral outer capsid / symbiont entry into host cell via permeabilization of host membrane / host cell endoplasmic reticulum / virion attachment to host cell / host cell plasma membrane
Similarity search - Function
Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Outer capsid protein VP4
Similarity search - Component
Biological speciesHuman rotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsXu, S. / Stuckert, M. / Burnside, R. / McGinnis, K. / Jiang, X. / Kennedy, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural basis of P[II] rotavirus evolution and host ranges under selection of histo-blood group antigens.
Authors: Xu, S. / McGinnis, K.R. / Liu, Y. / Huang, P. / Tan, M. / Stuckert, M.R. / Burnside, R.E. / Jacob, E.G. / Ni, S. / Jiang, X. / Kennedy, M.A.
History
DepositionOct 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer capsid protein VP4
B: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6744
Polymers36,6742
Non-polymers2,0002
Water81145
1
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3372
Polymers18,3371
Non-polymers1,0001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3372
Polymers18,3371
Non-polymers1,0001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.319, 38.432, 55.808
Angle α, β, γ (deg.)104.730, 90.110, 96.040
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 2 - 158 / Label seq-ID: 2 - 158

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Outer capsid protein VP4


Mass: 18337.139 Da / Num. of mol.: 2 / Fragment: VP4 haemagglut domain, residues 15-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rotavirus A / Gene: VP4 / Production host: Escherichia coli (E. coli) / References: UniProt: E9BVI9
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 999.912 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-2DGalpb1-3[LFucpa1-4]DGlcpNAcb1-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-3-2-4-4/a4-b1_b3-c1_c3-d1_c4-f1_d2-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}[(4+1)][a-L-Fucp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6, 25% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97932 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.54→53.95 Å / Num. obs: 9452 / % possible obs: 98.8 % / Redundancy: 6.6 % / CC1/2: 0.979 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.084 / Rrim(I) all: 0.221 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.54-2.586.30.4551.74840.840.2060.52399.8
6.89-53.966.90.09713.84760.9870.0420.1198.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UT9

6ut9


Resolution: 2.54→53.95 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.877 / SU B: 16.569 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 482 5.1 %RANDOM
Rwork0.2048 ---
obs0.2077 8970 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.43 Å2 / Biso mean: 25.953 Å2 / Biso min: 5.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å22.41 Å20.52 Å2
2--1.68 Å20.78 Å2
3----2.65 Å2
Refinement stepCycle: final / Resolution: 2.54→53.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2567 0 136 45 2748
Biso mean--25.67 19.87 -
Num. residues----317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0142781
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182427
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.7223800
X-RAY DIFFRACTIONr_angle_other_deg1.2241.6775618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.265315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74923.418158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47715417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.811514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023091
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02685
Refine LS restraints NCS

Ens-ID: 1 / Number: 4954 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.54→2.606 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 36 -
Rwork0.315 662 -
all-698 -
obs--99.15 %

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