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- PDB-5ha6: Crystal structure of human syncytin-1 fusion subunit -

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Basic information

Entry
Database: PDB / ID: 5ha6
TitleCrystal structure of human syncytin-1 fusion subunit
ComponentsSyncytin-1
KeywordsCELL ADHESION / glycoprotein / human / fusion
Function / homology
Function and homology information


syncytium formation by plasma membrane fusion / syncytium formation / myoblast fusion / anatomical structure morphogenesis / plasma membrane
Similarity search - Function
ENV polyprotein (coat polyprotein) / TLV/ENV coat polyprotein / Helix Hairpins - #210 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0006 Å
AuthorsAydin, H. / Lee, J.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)CIHR MOP-115066 Canada
CitationJournal: To Be Published
Title: Structural and functional characterization of the human Syncytin 1 fusion protein
Authors: Aydin, H. / Thavalingam, A. / Bikopoulos, G. / Sultana, A. / Lee, J.E.
History
DepositionDec 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Syncytin-1
B: Syncytin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7074
Polymers26,6362
Non-polymers712
Water1,31573
1
A: Syncytin-1
hetero molecules

A: Syncytin-1
hetero molecules

A: Syncytin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0606
Polymers39,9543
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area9450 Å2
ΔGint-84 kcal/mol
Surface area12730 Å2
MethodPISA
2
B: Syncytin-1
hetero molecules

B: Syncytin-1
hetero molecules

B: Syncytin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0606
Polymers39,9543
Non-polymers1063
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8320 Å2
ΔGint-74 kcal/mol
Surface area11340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.118, 48.118, 378.911
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-501-

CL

21B-501-

CL

31A-638-

HOH

41A-666-

HOH

DetailsTrimer determined by size exclusion chromatography

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Components

#1: Protein Syncytin-1 / Endogenous retrovirus group W member 1 / Env-W / Envelope polyprotein gPr73 / Enverin / HERV-7q ...Endogenous retrovirus group W member 1 / Env-W / Envelope polyprotein gPr73 / Enverin / HERV-7q Envelope protein / HERV-W envelope protein / HERV-W_7q21.2 provirus ancestral Env polyprotein / Syncytin


Mass: 13317.877 Da / Num. of mol.: 2 / Mutation: C405S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERVW-1, ERVWE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UQF0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.58 Å3/Da / Density % sol: 22.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 5% (w/v) PEG 3350, 0.1 M Sodium Acetate-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.84592 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84592 Å / Relative weight: 1
ReflectionResolution: 2→42.1 Å / Num. obs: 12052 / % possible obs: 99.7 % / Redundancy: 10.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.025 / Net I/σ(I): 20.9 / Num. measured all: 126807
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.058.80.751372028220.780.25796.1
8.95-42.18.10.0354.214531800.9990.0199.5

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Processing

Software
NameVersionClassification
Aimless0.5.8data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JF3

4jf3


Resolution: 2.0006→41.422 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 576 4.78 %random selection
Rwork0.1988 11466 --
obs0.2005 12042 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.21 Å2 / Biso mean: 43.2713 Å2 / Biso min: 13.31 Å2
Refinement stepCycle: final / Resolution: 2.0006→41.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1317 0 2 73 1392
Biso mean--38.03 39.6 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131334
X-RAY DIFFRACTIONf_angle_d1.2661798
X-RAY DIFFRACTIONf_chiral_restr0.053212
X-RAY DIFFRACTIONf_plane_restr0.006238
X-RAY DIFFRACTIONf_dihedral_angle_d14.815497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0006-2.20190.23361390.18452765290499
2.2019-2.52050.23031330.181928332966100
2.5205-3.17540.2481500.208328533003100
3.1754-41.43050.22751540.202330153169100
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)
11.1373-0.0745-0.05130.97050.80125.3874-0.0754-0.0893-0.04750.1-0.04820.03640.046-0.31360.14990.1511-0.00760.01170.14340.01480.213519.2009-12.81345.8834
22.7286-1.068-2.71531.86421.82943.109-0.0260.1835-0.3563-0.2269-0.0579-0.03820.503-0.28670.21240.2837-0.0125-0.01460.2406-0.02340.275822.8816-24.8589-12.91
32.5406-0.5959-0.44864.58663.24528.0011-0.1648-0.29570.00190.4459-0.13050.21470.2608-0.78390.4040.1821-0.00920.02710.2912-0.00340.257411.9457-16.342121.1999
41.76450.43-0.16831.9912-0.65740.4421-0.3178-0.36230.1980.42080.0444-0.169-0.46860.4265-0.08110.630.0888-0.06010.6431-0.00460.3065.24630.812651.6148
56.69812.28682.77313.7146-3.08026.6795-0.867-0.0795-0.0622-0.29690.1980.41573.62630.30640.59160.97210.1043-0.05070.6230.11810.541.6089-9.155170.9838
63.40882.9621-0.78846.4103-1.97375.2601-0.6851-0.5252-0.35660.1520.1569-0.79320.1451-0.21740.56670.52140.13190.00240.54470.02030.333511.0164-4.932141.6041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 395 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 396 through 410 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 411 through 434 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 388 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 389 through 410 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 411 through 434 )B0

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