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- PDB-6rx3: Crystal structure of human syncytin 2 in post-fusion conformation -

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Basic information

Entry
Database: PDB / ID: 6rx3
TitleCrystal structure of human syncytin 2 in post-fusion conformation
ComponentsSyncytin-2
KeywordsMEMBRANE PROTEIN / HUMAN PLACENTAL PROTEIN / MEMBRANE FUSION / ENDOGENOUS RETROVIRUS / HERV-FRD / SYNCYTIN
Function / homology
Function and homology information


syncytium formation / syncytium formation by plasma membrane fusion / myoblast fusion / 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: 2.2 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 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Syncytin-2
B: Syncytin-2
C: Syncytin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6264
Polymers36,5903
Non-polymers351
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, trimer determined by size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-86 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.416, 91.416, 69.725
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Syncytin-2 / Endogenous retrovirus group FRD member 1 / Envelope polyprotein / HERV-FRD / HERV-FRD_6p24.1 ...Endogenous retrovirus group FRD member 1 / Envelope polyprotein / HERV-FRD / HERV-FRD_6p24.1 provirus ancestral Env polyprotein


Mass: 12196.797 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: N-ter His-tag:MHHHHHH TEV cleavage site: ENLYFQS / Source: (gene. exp.) Homo sapiens (human) / Gene: ERVFRD-1, ERVFRDE1, UNQ6191/PRO20218 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P60508
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 25% v/v tert-butanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 10, 2017
RadiationMonochromator: cryogenically cooled channel-cut Si[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→45.7 Å / Num. obs: 17310 / % possible obs: 99.5 % / Redundancy: 11.3 % / Biso Wilson estimate: 57.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.053 / Rrim(I) all: 0.13 / Net I/σ(I): 11.5
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.1977 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1474 / CC1/2: 0.527 / Rpim(I) all: 0.873 / Rrim(I) all: 0.2164 / % possible all: 99

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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: 6RX1

6rx1


Resolution: 2.2→45.7 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.254 / SU Rfree Blow DPI: 0.205 / SU Rfree Cruickshank DPI: 0.202
RfactorNum. reflection% reflectionSelection details
Rfree0.256 824 4.76 %RANDOM
Rwork0.214 ---
obs0.216 17303 99.2 %-
Displacement parametersBiso mean: 59.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.3686 Å20 Å20 Å2
2--1.3686 Å20 Å2
3----2.7373 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.2→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 1 117 2229
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012131HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.082872HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d802SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes75HARMONIC2
X-RAY DIFFRACTIONt_gen_planes299HARMONIC5
X-RAY DIFFRACTIONt_it2131HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion18.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion296SEMIHARMONIC5
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_contact2588SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.33 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2833 144 5.26 %
Rwork0.2446 2594 -
all0.2467 2738 -
obs--98.56 %

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