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- PDB-4ojd: Crystal structure of a C-terminally truncated trimeric ectodomain... -

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Basic information

Entry
Database: PDB / ID: 4ojd
TitleCrystal structure of a C-terminally truncated trimeric ectodomain of the C. elegans fusion protein EFF-1 G260A/D321E/D322E mutant
ComponentsEFF-1A
KeywordsMEMBRANE PROTEIN / class II fusion protein / membrane fusion protein / cell surface
Function / homology
Function and homology information


nematode male tail mating organ morphogenesis / fusogenic activity / EFF-1 complex / nematode pharyngeal muscle development / post-embryonic body morphogenesis / nematode male tail tip morphogenesis / cell-cell fusion / vulval development / egg-laying behavior / syncytium formation by plasma membrane fusion ...nematode male tail mating organ morphogenesis / fusogenic activity / EFF-1 complex / nematode pharyngeal muscle development / post-embryonic body morphogenesis / nematode male tail tip morphogenesis / cell-cell fusion / vulval development / egg-laying behavior / syncytium formation by plasma membrane fusion / embryonic body morphogenesis / cell-cell contact zone / locomotion / morphogenesis of an epithelium / 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
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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 / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 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
H: EFF-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1134
Polymers59,0841
Non-polymers1,0293
Water1,60389
1
H: EFF-1A
hetero molecules

H: EFF-1A
hetero molecules

H: EFF-1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,33912
Polymers177,2523
Non-polymers3,0879
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area22020 Å2
ΔGint45 kcal/mol
Surface area53980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.443, 132.443, 132.443
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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


Mass: 59083.879 Da / Num. of mol.: 1
Fragment: C-terminally truncated ectodomain, UNP residues 23-509
Mutation: G260A/D321E/D322E
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 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.28 Å3/Da / Density % sol: 62.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1M Sodium chloride, 0.1M Bicine pH9.0, 30% w/v PEG monomethylether 550 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.26→46.83 Å / Num. all: 36548 / Num. obs: 35378 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 51.58 Å2
Reflection shellResolution: 2.26→2.38 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.6 / % possible all: 78.4

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OJC

4ojc


Resolution: 2.26→46.83 Å / Cor.coef. Fo:Fc: 0.9382 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1776 5.02 %RANDOM
Rwork0.1978 ---
obs0.199 35346 96.85 %-
all-36496 --
Displacement parametersBiso mean: 50.73 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.285 Å
Refinement stepCycle: LAST / Resolution: 2.26→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 67 89 3677
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013687HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.254998HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1296SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes539HARMONIC5
X-RAY DIFFRACTIONt_it3687HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.85
X-RAY DIFFRACTIONt_other_torsion17.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion508SEMIHARMONIC5
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_contact4023SEMIHARMONIC4
LS refinement shellResolution: 2.26→2.33 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2376 84 4.56 %
Rwork0.2312 1760 -
all0.2315 1844 -
obs--96.85 %
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)
11.9708-0.81110.77641.80331.52170.7105-0.0993-0.0648-0.2870.1188-0.10660.23080.2408-0.2940.2059-0.0925-0.02590.0614-0.12620.0746-0.1079-52.5511-48.1083-33.7274
23.815-0.5165-0.98810.378-0.32212.8666-0.13930.0289-0.44790.0673-0.09830.14230.4027-0.14370.2376-0.0107-0.04080.0773-0.0340.0171-0.0024-49.8856-50.1219-30.9937
30.97351.48171.13162.05721.22421.05780.1192-0.154-0.09430.2397-0.0937-0.0670.143-0.1043-0.0255-0.0354-0.0042-0.00380.01570.0029-0.0707-13.817-15.41924.2748
42.1914-0.7175-2.90234.0438-2.7935.1904-0.0034-0.16230.4193-0.1324-0.1216-0.2522-0.38920.22590.1250.0483-0.0415-0.0117-0.0185-0.0648-0.0135-3.230510.65799.0182
50.01340.1196-0.55622.42121.28362.4832-0.0314-0.1883-0.00850.331-0.20090.13910.2869-0.48960.2323-0.0568-0.0235-0.00530.0658-0.0174-0.0521-17.5119-10.58578.881
60.94480.0550.459900.30220.61390.0924-0.1806-0.02130.1939-0.05340.01710.0429-0.0578-0.039-0.0672-0.00770.0412-0.03460.067-0.1003-44.1372-43.0503-17.1267
74.36-1.55340.521302.41870-0.0527-0.2526-0.50320.1497-0.016-0.10260.1885-0.16690.0687-0.0398-0.01840.0125-0.04990.0801-0.1045-42.1768-51.4447-23.945
80.2461.1687-0.14231.8605-2.64110.09790.0023-0.0669-0.08890.0825-0.01030.057-0.0294-0.0740.0080.1477-0.08790.1199-0.05310.14740.3016-47.9518-62.3439-25.8836
90.2647-1.7935-0.33430.00452.49371.0088-0.1228-0.10420.0325-0.19780.0466-0.0917-0.3562-0.1640.07620.07990.0509-0.0171-0.08730.0564-0.059-36.9814-39.7745-29.9036
103.1419-1.34781.47873.87432.49612.47070.1389-0.5443-0.26210.3785-0.11330.13650.2258-0.2019-0.02560.0322-0.1009-0.02130.08890.02830.0152-29.8137-28.542-7.1447
111.69272.22410.81972.77711.29911.57880.0552-0.1691-0.08320.1688-0.0412-0.11650.11870.0547-0.014-0.05250.008-0.0018-0.0330.0337-0.0779-18.6777-20.0908-2.9428
120-1.1755-2.66050-1.84950.16650.0286-0.22050.2780.0882-0.05940.117-0.1310.04960.03080.03010.0352-0.01820.021-0.0724-0.0613-12.10626.67539.5862
1301.2105-0.06380.95561.36520.4277-0.2347-0.20160.0923-0.2952-0.01040.1315-0.3484-0.09360.2450.09810.0378-0.08360.0422-0.02090.1273-26.4574-10.1543-1.3857
140.4798-0.2684-0.34641.23652.257200.0667-0.2101-0.0597-0.0263-0.08240.01340.1834-0.31530.0157-0.0465-0.07470.02340.03120.0686-0.0709-35.3929-34.052-14.0255
151.0139-2.7303-0.87970.3073-1.6362.80370.05420.2122-0.4826-0.0697-0.04160.26110.4176-0.3921-0.0127-0.0312-0.0151-0.01060.015-0.03030.0706-45.2872-49.9472-34.0047
160.55382.8972.84932.4508-2.85673.9361-0.00390.2644-0.0831-0.12330.0730.24910.5254-0.1084-0.0691-0.1671-0.119-0.0011-0.14290.0319-0.1415-58.1997-49.4887-34.5174
170-0.65241.43470.32161.01260.8976-0.015-0.5290.16060.2905-0.20210.2044-0.0649-0.22550.2171-0.09090.03430.07190.0237-0.013-0.0545-53.801-19.514-22.7268
180.9931-2.80030.08540-0.81140.0281-0.0311-0.2157-0.00870.3619-0.0420.17120.1592-0.11380.0731-0.061-0.03130.10980.0015-0.0623-0.0603-60.903-25.4449-20.5937
192.26951.3013-0.41514.9706-0.20430.9592-0.0125-0.17990.11280.0572-0.11750.3474-0.1342-0.17370.13-0.10180.07170.02660.0048-0.0052-0.051-57.2163-23.2939-29.9557
205.9077-0.5883-1.34891.3171-1.86180.00020.0802-0.05830.3223-0.0805-0.07960.0689-0.1662-0.1744-0.0006-0.11450.09030.0693-0.0643-0.03130.0193-56.7875-14.6563-25.2868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{H|34 - 52}H34 - 52
2X-RAY DIFFRACTION2{H|53 - 109}H53 - 109
3X-RAY DIFFRACTION3{H|110 - 170}H110 - 170
4X-RAY DIFFRACTION4{H|171 - 182}H171 - 182
5X-RAY DIFFRACTION5{H|183 - 196}H183 - 196
6X-RAY DIFFRACTION6{H|197 - 226}H197 - 226
7X-RAY DIFFRACTION7{H|227 - 247}H227 - 247
8X-RAY DIFFRACTION8{H|248 - 252}H248 - 252
9X-RAY DIFFRACTION9{H|253 - 265}H253 - 265
10X-RAY DIFFRACTION10{H|266 - 280}H266 - 280
11X-RAY DIFFRACTION11{H|281 - 325}H281 - 325
12X-RAY DIFFRACTION12{H|326 - 332}H326 - 332
13X-RAY DIFFRACTION13{H|333 - 359}H333 - 359
14X-RAY DIFFRACTION14{H|360 - 382}H360 - 382
15X-RAY DIFFRACTION15{H|383 - 398}H383 - 398
16X-RAY DIFFRACTION16{H|399 - 408}H399 - 408
17X-RAY DIFFRACTION17{H|409 - 427}H409 - 427
18X-RAY DIFFRACTION18{H|428 - 433}H428 - 433
19X-RAY DIFFRACTION19{H|434 - 493}H434 - 493
20X-RAY DIFFRACTION20{H|494 - 510}H494 - 510

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