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- PDB-5ow3: Crystal structure of a C-terminally truncated trimeric ectodomain... -

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Basic information

Entry
Database: PDB / ID: 5ow3
TitleCrystal structure of a C-terminally truncated trimeric ectodomain of the Arabidopsis thaliana gamete fusion protein HAP2
ComponentsProtein HAPLESS 2
KeywordsMEMBRANE PROTEIN / Gamete fusion protein / class II fold / HAP2 / Membrane fusion
Function / homology
Function and homology information


pollen sperm cell differentiation / fusion of sperm to egg plasma membrane involved in double fertilization forming a zygote and endosperm / double fertilization forming a zygote and endosperm / plasma membrane fusion / plasma membrane => GO:0005886 / lipid binding / endoplasmic reticulum membrane / endoplasmic reticulum / plasma membrane
Similarity search - Function
Generative cell specific-1/HAP2 domain / Male gamete fusion factor / HAP2/GCS1
Similarity search - Domain/homology
ACETATE ION / Protein HAPLESS 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsFedry, J. / Legrand, P. / Rey, F.A. / Krey, T.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council340371 (CelCelFus) France
CitationJournal: PLoS Biol. / Year: 2018
Title: Evolutionary diversification of the HAP2 membrane insertion motifs to drive gamete fusion across eukaryotes.
Authors: Fedry, J. / Forcina, J. / Legrand, P. / Pehau-Arnaudet, G. / Haouz, A. / Johnson, M. / Rey, F.A. / Krey, T.
History
DepositionAug 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Protein HAPLESS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,98812
Polymers57,8301
Non-polymers1,15811
Water77543
1
C: Protein HAPLESS 2
hetero molecules

C: Protein HAPLESS 2
hetero molecules

C: Protein HAPLESS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,96536
Polymers173,4913
Non-polymers3,47433
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area23270 Å2
ΔGint-317 kcal/mol
Surface area58680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.255, 77.255, 219.526
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11C-1132-

HOH

21C-1140-

HOH

31C-1143-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules C

#1: Protein Protein HAPLESS 2 / GENERATIVE CELL SPECIFIC 1


Mass: 57830.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HAP2, GCS1, At4g11720, T5C23 / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: F4JP36
#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.: 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

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Non-polymers , 4 types, 52 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsResidues MET7 - GLY24 correspond to the signal peptide

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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: 3.27 Å3/Da / Density % sol: 62.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 100 mM Sodium Citrate pH 4.5 200 mM zinc acetate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 21328 / % possible obs: 56.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 63.42 Å2 / CC1/2: 0.995 / Net I/σ(I): 7.83
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.25 / Num. unique obs: 463 / CC1/2: 0.325 / % possible all: 16.7

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MF1

5mf1


Resolution: 2.75→42.43 Å / Cor.coef. Fo:Fc: 0.8594 / Cor.coef. Fo:Fc free: 0.7845 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.519
RfactorNum. reflection% reflectionSelection details
Rfree0.2774 520 4.88 %RANDOM
Rwork0.231 ---
obs0.2332 10646 55.36 %-
Displacement parametersBiso mean: 67.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.6453 Å20 Å20 Å2
2---4.6453 Å20 Å2
3---9.2905 Å2
Refine analyzeLuzzati coordinate error obs: 0.506 Å
Refinement stepCycle: 1 / Resolution: 2.75→42.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3511 0 65 43 3619
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073651HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.914944HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1268SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes524HARMONIC5
X-RAY DIFFRACTIONt_it3651HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.68
X-RAY DIFFRACTIONt_other_torsion19.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion491SEMIHARMONIC5
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_contact3732SEMIHARMONIC4
LS refinement shellResolution: 2.75→3.07 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2962 58 6.24 %
Rwork0.2552 871 -
all0.2578 929 -
obs--17.11 %

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