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- PDB-7s0k: HAP2 from Cyanidioschyzon merolae -

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Basic information

Entry
Database: PDB / ID: 7s0k
TitleHAP2 from Cyanidioschyzon merolae
ComponentsHAP2-GCS1 domain-containing protein
KeywordsMEMBRANE PROTEIN / Gamete fusogen / Class II fusion protein
Function / homologyGenerative cell specific-1/HAP2 domain / Male gamete fusion factor / HAP2/GCS1 / single fertilization / lipid binding / plasma membrane / DI(HYDROXYETHYL)ETHER / Generative cell specific-1/HAP2 domain-containing protein
Function and homology information
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFeng, J. / Dong, X.C. / Springer, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: Nat Commun / Year: 2022
Title: Monomeric prefusion structure of an extremophile gamete fusogen and stepwise formation of the postfusion trimeric state.
Authors: Feng, J. / Dong, X. / Su, Y. / Lu, C. / Springer, T.A.
History
DepositionAug 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HAP2-GCS1 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0528
Polymers59,4311
Non-polymers1,6217
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint17 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.960, 197.010, 74.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HAP2-GCS1 domain-containing protein


Mass: 59431.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon merolae (eukaryote) / Gene: CYME_CMK076C / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: M1V8A6

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-2-3/a4-b1_b4-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 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.: 1 / 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

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Non-polymers , 3 types, 78 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: PEG3350, isopropanol, glycerol, sodium citrate / PH range: 6.2-6.6

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0331 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2.3→45.63 Å / Num. obs: 33534 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.993 / Net I/σ(I): 7.11
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.2426 / Mean I/σ(I) obs: 0.45 / Num. unique obs: 2329 / CC1/2: 0.225 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
Cootmodel building
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6DBS

6dbs


Resolution: 2.3→45.63 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 1694 5.06 %
Rwork0.223 --
obs0.226 33497 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.79 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 107 73 3930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.42891410.39592480X-RAY DIFFRACTION95
2.37-2.450.42941310.38612649X-RAY DIFFRACTION99
2.45-2.530.36591370.34982628X-RAY DIFFRACTION99
2.53-2.630.39741320.34252647X-RAY DIFFRACTION100
2.63-2.750.41241430.36592642X-RAY DIFFRACTION100
2.75-2.90.35841450.2992622X-RAY DIFFRACTION99
2.9-3.080.31881440.26692629X-RAY DIFFRACTION99
3.08-3.320.28081420.25742665X-RAY DIFFRACTION100
3.32-3.650.25761310.20672679X-RAY DIFFRACTION100
3.65-4.180.26231500.18612665X-RAY DIFFRACTION99
4.18-5.260.21671440.1662708X-RAY DIFFRACTION99
5.27-45.630.20981540.20522789X-RAY DIFFRACTION98
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)
12.58312.0302-0.84322.7141-0.80920.58380.0022-0.1265-0.37450.1438-0.0581-0.06540.0730.04920.06220.40530.0170.02120.51450.02620.44515.22931.4733.143
25.73150.26631.75041.13461.06093.0098-0.3981-0.20590.9892-0.09190.22881.5665-0.2891-1.07260.23230.70180.0645-0.08080.98640.25681.6941-37.699-26.60829.612
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 37:461
2X-RAY DIFFRACTION2CHAIN A AND RESID 466:560

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