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- PDB-7ta2: Crystal structure of the human sperm-expressed surface protein SPACA6 -

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Basic information

Entry
Database: PDB / ID: 7ta2
TitleCrystal structure of the human sperm-expressed surface protein SPACA6
ComponentsSperm acrosome membrane-associated protein 6
KeywordsUNKNOWN FUNCTION / Gamete fusion / sperm / fusogen / fertilization
Function / homologySperm acrosome membrane-associated protein 6 / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / BROMIDE ION / Sperm acrosome membrane-associated protein 6
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsVance, T.D.R. / Yip, P. / Jimenez, E. / Uson, I. / Lee, J.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-153281 Canada
CitationJournal: Commun Biol / Year: 2022
Title: SPACA6 ectodomain structure reveals a conserved superfamily of gamete fusion-associated proteins.
Authors: Vance, T.D.R. / Yip, P. / Jimenez, E. / Li, S. / Gawol, D. / Byrnes, J. / Uson, I. / Ziyyat, A. / Lee, J.E.
History
DepositionDec 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 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
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: Sperm acrosome membrane-associated protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,83911
Polymers27,0401
Non-polymers79910
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.984, 46.522, 167.670
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 acrosome membrane-associated protein 6 / BACHELOR-like protein


Mass: 27039.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPACA6, SPACA6P, UNQ2487/PRO5774 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: W5XKT8
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
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: 1.96 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Ammonium chloride, PEG 3350, FOS-choline-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.91165 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91165 Å / Relative weight: 1
ReflectionResolution: 2.25→44.83 Å / Num. obs: 11487 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.041 / Rrim(I) all: 0.116 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.25-2.326.70.75410290.8710.3030.815100
9-44.835.90.0462340.9990.0180.0599.7

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
DIALSv2.2.0data reduction
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JK9

5jk9


Resolution: 2.25→44.83 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 583 5.1 %
Rwork0.2011 10848 -
obs0.2037 11431 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.54 Å2 / Biso mean: 48.4307 Å2 / Biso min: 14.38 Å2
Refinement stepCycle: final / Resolution: 2.25→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 10 65 1811
Biso mean--53.3 34.41 -
Num. residues----220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.25-2.480.29381540.211426282782
2.48-2.830.26941540.205426402794
2.84-3.570.25531350.199327162851
3.57-44.830.24111400.198528643004
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)
14.25120.57332.42712.27610.66738.34290.14160.57060.1614-0.7672-0.29480.34780.53630.63380.13490.61960.1085-0.13460.54240.05710.28055.91897.1046-9.1334
23.44280.52371.42232.643-0.4254.51050.31810.3479-0.3745-0.2992-0.11710.27930.6036-0.2534-0.17810.4120.056-0.06120.48880.01050.27798.4462.5346-0.8469
31.1278-0.0737-0.25920.45630.98625.0686-0.00780.3287-0.3402-0.4379-0.17090.14080.55220.17210.12770.63890.1158-0.05280.3503-0.04770.32919.9915-2.10028.0733
49.92040.33868.13381.66240.29426.90560.3386-0.1442-0.15430.03930.20980.03020.498-0.7643-0.46160.29090.04270.03270.36580.08030.27135.67897.369816.1703
53.37912.07182.72653.79662.76567.2139-0.0684-0.0630.06910.4613-0.188-0.23250.3060.23590.29560.21260.0474-0.04350.14880.04840.3576.304511.212546.0968
63.2771-1.5497-1.31243.8292.52674.42420.052-0.00710.3547-0.01340.1236-0.298-0.22780.219-0.13920.1225-0.0446-0.01210.12010.05330.24747.901718.692140.8817
73.77850.1658-0.76554.92591.40578.8472-0.0131-0.11470.05050.45760.0801-0.2149-0.5772-0.00370.04650.1824-0.0088-0.05160.0618-0.0060.26837.548917.67546.271
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 49 )A27 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 95 )A50 - 95
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 131 )A96 - 131
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 145 )A132 - 145
5X-RAY DIFFRACTION5chain 'A' and (resid 146 through 169 )A146 - 169
6X-RAY DIFFRACTION6chain 'A' and (resid 170 through 209 )A170 - 209
7X-RAY DIFFRACTION7chain 'A' and (resid 210 through 246 )A210 - 246

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