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- PDB-6rx1: Crystal structure of human syncytin 1 in post-fusion conformation -

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Basic information

Entry
Database: PDB / ID: 6rx1
TitleCrystal structure of human syncytin 1 in post-fusion conformation
ComponentsSyncytin-1
KeywordsMEMBRANE PROTEIN / HUMAN PLACENTAL PROTEIN / MEMBRANE FUSION / ENDOGENOUS RETROVIRUS / HERV-W / SYNCYTIN
Function / homology
Function and homology information


syncytium formation / syncytium formation by plasma membrane fusion / 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: 2.1 Å
AuthorsRuigrok, K. / Backovic, M. / Vaney, M.C. / Rey, F.A.
Funding support France, 1items
OrganizationGrant numberCountry
European Research Council340371 France
Citation
Journal: J.Mol.Biol. / Year: 2019
Title: X-ray Structures of the Post-fusion 6-Helix Bundle of the Human Syncytins and their Functional Implications.
Authors: Ruigrok, K. / Vaney, M.C. / Buchrieser, J. / Baquero, E. / Hellert, J. / Baron, B. / England, P. / Schwartz, O. / Rey, F.A. / Backovic, M.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of a pivotal domain of human syncytin-2, a 40 million years old endogenous retrovirus fusogenic envelope gene captured by primates.
Authors: Renard, M. / Varela, P.F. / Letzelter, C. / Duquerroy, S. / Rey, F.A. / Heidmann, T.
History
DepositionJun 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 2024Group: 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
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

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Assembly

Deposited unit
A: Syncytin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7423
Polymers12,6141
Non-polymers1282
Water1,26170
1
A: Syncytin-1
hetero molecules

A: Syncytin-1
hetero molecules

A: Syncytin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2259
Polymers37,8423
Non-polymers3836
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 area9760 Å2
ΔGint-94 kcal/mol
Surface area13460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.416, 50.416, 260.199
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-502-

CL

21A-603-

HOH

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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: 12614.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The following sequence MHHHHHHENLYFQS at the N-terminal of the protein sequence is from an expression tag with the 1st residue MET as the initiating methionine. The 3 first residues 'TST' ...Details: The following sequence MHHHHHHENLYFQS at the N-terminal of the protein sequence is from an expression tag with the 1st residue MET as the initiating methionine. The 3 first residues 'TST' from the protein sequence are disordered in density.
Source: (gene. exp.) Homo sapiens (human) / Gene: ERVW-1, ERVWE1 / Plasmid: PET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UQF0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 30% v/v 2-propanol, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.070638 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 17, 2016
RadiationMonochromator: cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a KirkpatrickBaez pair of focussing mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.070638 Å / Relative weight: 1
ReflectionResolution: 2.1→43.1 Å / Num. obs: 7752 / % possible obs: 99.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 30 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.08 / Rrim(I) all: 0.15 / Net I/σ(I): 7
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 622 / CC1/2: 0.47 / Rpim(I) all: 0.81 / Rrim(I) all: 1.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSv2016data reduction
Aimless0.5.28data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y4M

1y4m


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.212 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.164
RfactorNum. reflection% reflectionSelection details
Rfree0.242 369 4.77 %RANDOM
Rwork0.216 ---
obs0.217 7735 98.3 %-
Displacement parametersBiso max: 154.08 Å2 / Biso mean: 50.38 Å2 / Biso min: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.886 Å20 Å20 Å2
2---0.886 Å20 Å2
3---1.7719 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms717 0 7 70 794
Biso mean--79.45 59.81 -
Num. residues----89
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d278SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes25HARMONIC2
X-RAY DIFFRACTIONt_gen_planes103HARMONIC5
X-RAY DIFFRACTIONt_it728HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion91SEMIHARMONIC5
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_contact900SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d728HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg977HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion16.55
LS refinement shellResolution: 2.1→2.35 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2544 103 4.75 %
Rwork0.2116 2064 -
all0.2136 2167 -
obs--99.5 %

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