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- PDB-5mf1: Crystal structure of a C-terminally truncated trimeric ectodomain... -

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Basic information

Entry
Database: PDB / ID: 5mf1
TitleCrystal structure of a C-terminally truncated trimeric ectodomain of the Chlamydomonas reinhardtii gamete fusion protein HAP2
ComponentsFusion protein HAP2/GCS1
KeywordsMEMBRANE PROTEIN / class II membrane fusion protein / type I transmembrane protein / glycoprotein
Function / homology
Function and homology information


fusion of sperm to egg plasma membrane involved in single fertilization / cell projection membrane / protein insertion into membrane / cytoplasmic vesicle membrane / cytoplasmic vesicle / lipid binding / plasma membrane
Similarity search - Function
Generative cell specific-1/HAP2 domain / Male gamete fusion factor / HAP2/GCS1
Similarity search - Domain/homology
2-acetamido-2-deoxy-beta-D-galactopyranose / Hapless 2
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.3 Å
AuthorsFedry, J. / Rey, F.A. / Krey, T.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council"CelCelFus" France
CitationJournal: Cell / Year: 2017
Title: The Ancient Gamete Fusogen HAP2 Is a Eukaryotic Class II Fusion Protein.
Authors: Fedry, J. / Liu, Y. / Pehau-Arnaudet, G. / Pei, J. / Li, W. / Tortorici, M.A. / Traincard, F. / Meola, A. / Bricogne, G. / Grishin, N.V. / Snell, W.J. / Rey, F.A. / Krey, T.
History
DepositionNov 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Jul 29, 2020Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_audit_support / 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_audit_support.funding_organization / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion protein HAP2/GCS1
B: Fusion protein HAP2/GCS1
C: Fusion protein HAP2/GCS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,5879
Polymers193,2593
Non-polymers1,3276
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17370 Å2
ΔGint-60 kcal/mol
Surface area50290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.970, 114.060, 137.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fusion protein HAP2/GCS1


Mass: 64419.812 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: HAP2/GCS1 / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A4GRC6
#2: 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.: 3
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: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH7.5 2% 2-Propanol 100 mM sodium acetate 12-14%w/v PEG 8000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 3.3→48.62 Å / Num. obs: 25181 / % possible obs: 99.59 % / Redundancy: 4.86 % / Biso Wilson estimate: 93.84 Å2 / CC1/2: 0.989 / Rpim(I) all: 0.1051 / Net I/σ(I): 7.49
Reflection shellResolution: 3.3→3.418 Å / Redundancy: 4.9 % / CC1/2: 0.421 / Rpim(I) all: 0.6426 / % possible all: 99.07

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.3→48.62 Å / Cor.coef. Fo:Fc: 0.8893 / Cor.coef. Fo:Fc free: 0.833 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.543
RfactorNum. reflection% reflectionSelection details
Rfree0.2662 1259 5 %RANDOM
Rwork0.219 ---
obs0.2213 25161 99.76 %-
Displacement parametersBiso mean: 88.79 Å2
Baniso -1Baniso -2Baniso -3
1-21.9868 Å20 Å20 Å2
2---8.3628 Å20 Å2
3----13.624 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: 1 / Resolution: 3.3→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9948 0 84 0 10032
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00810246HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1213969HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3407SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes215HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1499HARMONIC5
X-RAY DIFFRACTIONt_it10246HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.36
X-RAY DIFFRACTIONt_other_torsion18.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1390SEMIHARMONIC5
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_contact11590SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.44 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2741 140 5.02 %
Rwork0.249 2650 -
all0.2502 2790 -
obs--99.04 %

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