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- PDB-1y4m: Crystal structure of human endogenous retrovirus HERV-FRD envelop... -

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Basic information

Entry
Database: PDB / ID: 1y4m
TitleCrystal structure of human endogenous retrovirus HERV-FRD envelope protein (syncitin-2)
ComponentsHERV-FRD_6p24.1 provirus ancestral Env polyprotein
KeywordsMEMBRANE PROTEIN / Coat protein / membrane fusion / endogenous retrovirus
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: 1.6 Å
AuthorsRenard, M. / Varela, P.F. / Letzelter, C. / Duquerroy, S. / Rey, F.A. / Heidmann, T.
CitationJournal: 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
DepositionDec 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 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: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
B: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
C: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4054
Polymers17,3693
Non-polymers351
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-68 kcal/mol
Surface area8710 Å2
MethodPISA
2
A: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
B: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
C: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
hetero molecules

A: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
B: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
C: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
hetero molecules

A: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
B: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
C: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
hetero molecules

A: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
B: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
C: HERV-FRD_6p24.1 provirus ancestral Env polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,61916
Polymers69,47712
Non-polymers1424
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area27010 Å2
ΔGint-268 kcal/mol
Surface area29260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.404, 90.404, 38.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11B-117-

HOH

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Components

#1: Protein HERV-FRD_6p24.1 provirus ancestral Env polyprotein / Envelope polyprotein / HERV-FRD / Syncytin 2 / UNQ6191/PRO20218


Mass: 5789.728 Da / Num. of mol.: 3
Fragment: Ectodomain of the transmembrane subunit (residues 391-443).
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERVFRDE1 / Plasmid: pET28(+)b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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.: 101 / 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: 2.275 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Sodium Chloride, Sodium Acetate tri-hydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.95375 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 28, 2004 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95375 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 22623 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.2 Å2
Reflection shellResolution: 1.53→1.58 Å / % possible all: 75.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MOF

1mof


Resolution: 1.6→31.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1074573.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1998 10 %RANDOM
Rwork0.248 ---
all0.262 23835 --
obs0.248 19988 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.2406 Å2 / ksol: 0.383905 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1--7.44 Å20 Å20 Å2
2---7.44 Å20 Å2
3---14.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.6→31.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 1 101 1300
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.57
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it3.032.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.289 282 9.7 %
Rwork0.275 2613 -
obs--84 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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