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- PDB-4ojc: Crystal structure of the wild-type full-length trimeric ectodomai... -

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Basic information

Entry
Database: PDB / ID: 4ojc
TitleCrystal structure of the wild-type full-length trimeric ectodomain of the C. elegans fusion protein EFF-1
ComponentsEFF-1A
KeywordsMEMBRANE PROTEIN / class II fusion protein / membrane fusion protein / cell surface
Function / homology
Function and homology information


post-embryonic body morphogenesis / nematode male tail mating organ morphogenesis / fusogenic activity / nematode pharyngeal muscle development / nematode male tail tip morphogenesis / cell-cell fusion / vulval development / syncytium formation by cell-cell fusion / embryonic body morphogenesis / egg-laying behavior ...post-embryonic body morphogenesis / nematode male tail mating organ morphogenesis / fusogenic activity / nematode pharyngeal muscle development / nematode male tail tip morphogenesis / cell-cell fusion / vulval development / syncytium formation by cell-cell fusion / embryonic body morphogenesis / egg-laying behavior / cell-cell contact zone / morphogenesis of an epithelium / locomotion / kinase activity / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Cell-cell fusogen EFF/AFF, domain 3 / Cell-cell fusogen EFF/AFF, domain 1 / Cell-cell fusogen EFF/AFF / Cell-cell fusogen EFF/AFF, domain 3 / Type I membrane glycoproteins cell-cell fusogen / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein kinase domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.93 Å
AuthorsKrey, T. / Rey, F.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Structural basis of eukaryotic cell-cell fusion
Authors: Perez-Vargas, J. / Krey, T. / Valansi, C. / Avinoam, O. / Haouz, A. / Jamin, M. / Raveh-Barak, H. / Podbilewicz, B. / Rey, F.A.
History
DepositionJan 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EFF-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,90014
Polymers64,9481
Non-polymers1,95313
Water34219
1
A: EFF-1A
hetero molecules

A: EFF-1A
hetero molecules

A: EFF-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,70142
Polymers194,8433
Non-polymers5,85839
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area27780 Å2
ΔGint-366 kcal/mol
Surface area55750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.698, 173.698, 173.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-1106-

SO4

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Components

#1: Protein EFF-1A / Protein EFF-1 / isoform a


Mass: 64947.637 Da / Num. of mol.: 1 / Fragment: UNP residues 23-561
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: C26D10.5, CELE_C26D10.5, eff-1 / Plasmid: pMT-based / Cell (production host): S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: G5ECA1
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.36 Å3/Da / Density % sol: 63.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2% 2-Propanol, 50mM sodium citrate, 0.8-1.2M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0396 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2010
RadiationMonochromator: LN2 cooled Fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0396 Å / Relative weight: 1
ReflectionResolution: 2.93→50 Å / Num. all: 18909 / Num. obs: 18417 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 113.4 Å2
Reflection shellResolution: 2.93→3.09 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 2735

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
BUSTER2.9.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.93→46.42 Å / Cor.coef. Fo:Fc: 0.9231 / Cor.coef. Fo:Fc free: 0.8869 / SU R Cruickshank DPI: 0.814 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2776 906 5.16 %RANDOM
Rwork0.2199 ---
all0.2227 18901 --
obs0.2227 17553 92.87 %-
Displacement parametersBiso mean: 92.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.549 Å
Refinement stepCycle: LAST / Resolution: 2.93→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 115 19 3773
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013833HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.345195HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1296SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes93HARMONIC2
X-RAY DIFFRACTIONt_gen_planes560HARMONIC5
X-RAY DIFFRACTIONt_it3833HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion22.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion528SEMIHARMONIC5
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_contact4121SEMIHARMONIC4
LS refinement shellResolution: 2.93→3.11 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3892 140 5.57 %
Rwork0.3102 2374 -
all0.3147 2514 -
obs--92.87 %

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