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- PDB-7ux0: Human Sperm TMEM95 Ectodomain -

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Basic information

Entry
Database: PDB / ID: 7ux0
TitleHuman Sperm TMEM95 Ectodomain
ComponentsSperm-egg fusion protein TMEM95
KeywordsCELL ADHESION / Fertilization / Sperm-egg binding / Sperm-egg fusion / Acrosomal membrane protein
Function / homologyTMEM95 family / TMEM95 family / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / sperm plasma membrane / TRIETHYLENE GLYCOL / Sperm-egg fusion protein TMEM95
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / molecular replacement / Resolution: 1.49 Å
AuthorsTang, S. / Kim, P.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)K99HD104924 United States
Damon Runyon Cancer Research FoundationDRG-2301-17 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Human sperm TMEM95 binds eggs and facilitates membrane fusion.
Authors: Tang, S. / Lu, Y. / Skinner, W.M. / Sanyal, M. / Lishko, P.V. / Ikawa, M. / Kim, P.S.
History
DepositionMay 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sperm-egg fusion protein TMEM95
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6883
Polymers13,8051
Non-polymers8832
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.530, 43.113, 72.018
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sperm-egg fusion protein TMEM95 / Transmembrane protein 95


Mass: 13805.021 Da / Num. of mol.: 1 / Fragment: ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMEM95, UNQ9390/PRO34281 / Production host: Homo sapiens (human) / References: UniProt: Q3KNT9
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 150 mM NaCl, 20 mM HEPES pH 7.3, 30 mM CaCl2, 2% (w/v) PPG-P400, and 22% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2021
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.49→36.01 Å / Num. obs: 20505 / % possible obs: 99.7 % / Redundancy: 12.6 % / CC1/2: 0.997 / Net I/σ(I): 12.3
Reflection shellResolution: 1.49→1.52 Å / Num. unique obs: 1004 / CC1/2: 0.855

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RESOLVEmodel building
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.49→36.01 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2505 972 4.75 %
Rwork0.2225 19503 -
obs0.2238 20475 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.92 Å2 / Biso mean: 30.2975 Å2 / Biso min: 11.95 Å2
Refinement stepCycle: final / Resolution: 1.49→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 59 89 1030
Biso mean--41.24 36.35 -
Num. residues----115
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.49-1.570.42551470.37172711285899
1.57-1.670.32191470.3282740288799
1.67-1.80.28261250.27652752287799
1.8-1.980.24751350.219327532888100
1.98-2.270.25871310.208527942925100
2.27-2.860.27731670.210827802947100
2.86-36.010.19461200.19662973309399

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