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- PDB-7sem: Structure-based design of prefusion-stabilized human metapneumovi... -

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Basic information

Entry
Database: PDB / ID: 7sem
TitleStructure-based design of prefusion-stabilized human metapneumovirus fusion proteins
Components
  • Fusion glycoprotein F0
  • MPE8 Fab heavy chain
  • MPE8 Fab light chain
KeywordsVIRAL PROTEIN/Immune System / human metapneumovirus / fusion protein / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHomo sapiens (human)
Human metapneumovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRush, S.A. / Hsieh, C.-L. / McLellan, J.S.
Funding support United States, 2items
OrganizationGrant numberCountry
Robert A. Welch FoundationF-0003-19620604 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins.
Authors: Hsieh, C.L. / Rush, S.A. / Palomo, C. / Chou, C.W. / Pickens, W. / Mas, V. / McLellan, J.S.
History
DepositionSep 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: MPE8 Fab heavy chain
F: Fusion glycoprotein F0
C: MPE8 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7796
Polymers107,1153
Non-polymers6643
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.169, 45.560, 176.270
Angle α, β, γ (deg.)90.000, 94.210, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z

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Components

#1: Antibody MPE8 Fab heavy chain


Mass: 23985.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293 / Production host: Homo sapiens (human)
#2: Protein Fusion glycoprotein F0 / Fusion glycoprotein F1 / Fusion glycoprotein F2


Mass: 60357.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human metapneumovirus / Cell (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: H6X1Z0
#3: Antibody MPE8 Fab light chain


Mass: 22772.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK293 / Production host: Homo sapiens (human)
#4: 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.: 3 / Source method: obtained synthetically / 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 nl of the complex (5.4 mg/ml) with 50 nl of reservoir solution containing 10% (v/v) isopropanol, 0.1 M HEPES pH 7.5, and 20% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→43.95 Å / Num. obs: 54115 / % possible obs: 97.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 39.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.057 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4437 / CC1/2: 0.693 / Rpim(I) all: 0.542

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5wb0, 5u68

5wb0

5u68


Resolution: 2.2→43.95 Å / SU ML: 0.2281 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.2286
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239 2545 4.71 %
Rwork0.2165 51528 -
obs0.2176 54073 97.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.24 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6380 0 42 173 6595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00846541
X-RAY DIFFRACTIONf_angle_d1.10678885
X-RAY DIFFRACTIONf_chiral_restr0.07071041
X-RAY DIFFRACTIONf_plane_restr0.01051135
X-RAY DIFFRACTIONf_dihedral_angle_d13.46272364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.33521530.30042813X-RAY DIFFRACTION98.41
2.24-2.290.27131330.30432923X-RAY DIFFRACTION97.92
2.29-2.340.29941430.28392828X-RAY DIFFRACTION98.18
2.34-2.390.31151390.28342896X-RAY DIFFRACTION98.89
2.39-2.450.32581210.27092819X-RAY DIFFRACTION96.81
2.45-2.520.28151290.25882897X-RAY DIFFRACTION97.52
2.52-2.590.27161530.2692762X-RAY DIFFRACTION96.36
2.59-2.680.28721360.25482712X-RAY DIFFRACTION92.2
2.68-2.770.27441720.2662851X-RAY DIFFRACTION98.92
2.77-2.880.28371480.26222914X-RAY DIFFRACTION98.71
2.88-3.010.30941320.24782884X-RAY DIFFRACTION98.34
3.01-3.170.24451340.24462863X-RAY DIFFRACTION97.4
3.17-3.370.21381560.22272822X-RAY DIFFRACTION96.16
3.37-3.630.23481480.22132777X-RAY DIFFRACTION94.88
3.63-40.22111470.20222943X-RAY DIFFRACTION99.23
4-4.570.1951330.16642957X-RAY DIFFRACTION97.88
4.57-5.760.19491320.17052847X-RAY DIFFRACTION94.81
5.76-43.950.22081360.18113020X-RAY DIFFRACTION96.99
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)
11.04478347494-0.2202983736621.614400150620.426811064678-0.1333686003542.220285152620.09812202231361.021058053140.018554324875-0.311647369794-0.0354653570503-0.01830599079430.05769589674420.308591404267-0.03969215581090.3565276387840.0395904804840.03426509279161.243411094650.01599798328870.3583277245426.68068406732-10.325840842524.576634564
21.387498667560.282989796557-0.3172967361141.09079586109-0.4249471195980.7073993572270.067787769297-0.04444478521380.01856939204240.1839583585690.0109183837528-0.0717602832375-0.02545694943980.01124361124-0.08696912666490.2171087277380.0331722080179-0.03218272272540.25466517132-0.02126411928320.21994093131428.1894732256-14.000409171670.538144058
30.9572095308720.294085776039-0.2905856588910.936348257619-0.3305737113842.27681645852-0.004590913899240.8336568991280.0571699644631-0.296675502002-0.03073634831390.1559734099690.183801732517-0.722694012147-0.007201927953920.267474740930.00477087462315-0.02399998918471.04695068943-0.02566793935250.313717999508-9.36587306742-14.100077698131.4350882858
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'B' and resid 1 through 214)BA1 - 2141 - 214
22(chain 'F' and resid 19 through 465)FB19 - 4651 - 430
33(chain 'C' and resid 2 through 208)CF2 - 2081 - 204

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