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

ID or keywords:

Entry

Database: PDB / ID: 4oje

Title

Crystal structure of a C-terminally truncated trimeric ectodomain of the C. elegans fusion protein EFF-1

Components

EFF-1A

Keywords

MEMBRANE 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 / chordate pharyngeal muscle development / post-embryonic body morphogenesis / nematode male tail tip morphogenesis / vulval development / cell-cell fusion / syncytium formation by plasma membrane fusion / embryonic body morphogenesis ...
Similarity search - Function

Biological species

Caenorhabditis elegans (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.57 Å

Authors

Krey, T. / Rey, F.A.

Citation

Journal: 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

Deposition	Jan 21, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	May 14, 2014	Provider: repository / Type: Initial release
Revision 2.0	Jul 29, 2020	Group: 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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4oje.cif.gz	199.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4oje.ent.gz	164.2 KB	Display	PDB format
PDBx/mmJSON format	4oje.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oj/4oje ftp://data.pdbj.org/pub/pdb/validation_reports/oj/4oje	HTTPS FTP

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Related structure data

Related structure data	4ojcC 4ojdC C: citing same article (ref.)
Similar structure data	4ojd-1 1jll-d 4adi-d 2nua-d 3jqm-d 4l2z-1 4gt0-1 4gsx-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

H: EFF-1A

hetero molecules

60.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

H: EFF-1A

hetero molecules

H: EFF-1A

hetero molecules

H: EFF-1A

hetero molecules

defined by author&software
180 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	106.886, 106.886, 135.620
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

#1: Protein

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

Mass: 59041.793 Da / Num. of mol.: 1
Fragment: C-terminally truncated ectodomain, UNP residues 23-509
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

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}	LINUCS	PDB-CARE

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#4: Chemical

ChemComp-PO4 / PHOSPHATE ION /

Phosphate

Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.79 Å³/Da / Density % sol: 67.53 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 11% PEG 3000, 16mM Na2HPO4, 84mM KH2PO4, 0.25% DDM, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0015 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2011
Radiation	Monochromator: LN2 cooled Fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0015 Å / Relative weight: 1
Reflection	Resolution: 2.56→50 Å / Num. all: 28048 / Num. obs: 27936 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / B_iso Wilson estimate: 65.19 Å²
Reflection shell	Resolution: 2.56→2.7 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 4075 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
XDS		data scaling
SHARP		phasing
BUSTER	2.11.2	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.57→49.72 Å / Cor.coef. F_o:F_c: 0.9193 / Cor.coef. F_o:F_c free: 0.9068 / SU R Cruickshank DPI: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2209	1403	5.03 %	RANDOM
R_work	0.1789	-	-	-
all	0.181	27994	-	-
obs	0.181	27879	99.59 %	-

Displacement parameters

B_iso mean: 65.98 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.8257 Å²	0 Å²	0 Å²
2-	-	-5.8257 Å²	0 Å²
3-	-	-	11.6513 Å²

Refine analyze

Luzzati coordinate error obs: 0.34 Å

Refinement step

Cycle: LAST / Resolution: 2.57→49.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3624	0	62	73	3759

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	3793	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.23	5143	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		1321	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		90	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		555	HARMONIC	5
X-RAY DIFFRACTION	t_it		3793	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.5
X-RAY DIFFRACTION	t_other_torsion	19.57
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		511	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		4120	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.57→2.67 Å / Total num. of bins used: 14

	R_factor	Num. reflection	% reflection
R_free	0.3276	142	5.01 %
R_work	0.234	2691	-
all	0.2387	2833	-
obs	-	2833	99.59 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.5824	3.2954	-2.7589	5.4985	-1.0422	1.3341	0.0936	-0.2442	0.308	0.6621	0.0627	0.5551	-0.4385	-0.3289	-0.1563	0.0763	0.0652	0.186	0.1311	-0.0681	-0.304	40.2532	-25.4924	15.6485
2	1.3728	1.3903	1.0286	3.8972	2.5224	6.422	0.0963	-0.3866	0.0947	0.7019	-0.0857	-0.1332	-0.435	-0.335	-0.0106	0.1614	0.0855	0.0682	0.1015	-0.0942	-0.2077	42.0169	-21.5202	14.3927
3	0.5941	0.2151	-0.7382	0.4192	0.8445	6.6866	-0.1284	0.2134	0.1066	-0.0891	-0.1084	0.1843	-0.3194	-0.5352	0.2368	-0.1974	0.0791	-0.0788	-0.2482	0.004	-0.2215	41.0031	-20.4459	-48.0156
4	1.5311	-1.9326	3.6566	2.1015	-0.5126	2.5488	-0.0168	0.3727	-0.4886	-0.7158	0.1813	0.0293	0.0253	0.0604	-0.1645	-0.0505	-0.0815	-0.0742	0.088	-0.0847	-0.2029	44.2902	-36.2496	-71.4167
5	4.145	0.8405	-0.404	2.3092	0.1829	5.2002	-0.1053	-0.4592	0.4646	0.0648	0.0594	0.2839	-0.1992	-0.7435	0.0459	-0.2686	0.0573	-0.0956	0.0162	-0.0667	-0.1903	35.3711	-23.7999	-50.5681
6	2.0739	-0.4178	0.125	1.767	-0.628	1.0076	-0.0382	-0.3974	-0.0026	0.5343	0.0639	0.547	-0.3726	-0.4431	-0.0257	-0.2343	0.055	0.1558	-0.2312	-0.0855	-0.2555	35.0268	-19.2398	-1.5582
7	-0.155	1.4486	3.7075	1.7243	-1.2201	0.6812	-0.0859	-0.7799	0.3539	0.3086	0.1862	0.4754	-0.4688	-0.2765	-0.1003	-0.0807	0.0432	0.0369	-0.2071	-0.121	-0.2406	41.74	-14.8581	5.9493
8	3.1333	-2.5167	-0.9423	-0.6819	2.8166	7.5894	0.1566	-0.1984	-0.292	-0.3271	0.142	0.3899	0.0975	-0.4901	-0.2986	0.254	0.0883	0.0364	0.1478	-0.1545	0.1204	39.817	-8.9098	17.341
9	-0.6021	-0.8409	0.1591	4.7193	3.4525	0.818	-0.2023	-0.0924	0.2353	0.6456	-0.2649	0.3701	0.4574	0.1867	0.4672	0.0463	-0.0102	0.0154	-0.057	-0.0744	-0.1023	48.5927	-25.3694	-0.4347
10	1.2802	3.6496	0.4408	3.7874	2.2097	4.4435	-0.0358	-0.1147	0.1992	0.0915	-0.0424	0.7435	-0.3815	-0.4277	0.0782	-0.0405	0.0545	0.0578	-0.0115	-0.0227	-0.0319	37.8451	-21.4185	-23.6716
11	1.5047	-0.4883	0.2085	0.4636	-0.3992	6.8617	-0.1759	-0.0918	0.1367	-0.0515	0.0158	0.0829	-0.4364	-0.3326	0.1601	-0.1917	0.0411	-0.0325	-0.2934	-0.0298	-0.1921	42.8873	-22.0852	-37.7277
12	7.4715	2.8877	-2.5415	0.8439	-1.4188	4.7541	-0.0151	0.2707	-0.0056	0.3101	0.1282	-0.107	-0.3367	-0.5053	-0.1131	-0.2125	-0.0889	-0.108	-0.0523	-0.1135	-0.2483	37.6817	-35.5791	-64.347
13	1.0043	-0.6576	0.425	-0.735	1.1037	0	-0.1125	0.0917	0.0043	-0.0443	0.0428	0.1762	0.5873	-0.2894	0.0697	-0.0747	-0.2149	0.0128	-0.0679	-0.077	-0.2047	35.5313	-32.2406	-39.8679
14	2.8198	1.6801	0.198	1	-1.1666	1.2341	0.0975	-0.1931	0.1651	0.1482	0.1181	0.6598	-0.3565	-0.471	-0.2156	-0.1626	0.079	0.0388	-0.1625	-0.0615	-0.2093	38.9999	-22.0144	-13.6555
15	2.2223	0.599	1.0653	-0.0491	3.9757	8.3154	-0.0601	-0.7799	0.1024	0.3086	0.212	0.0545	-0.7098	0.2186	-0.1519	0.3266	0.0062	0.1069	0.2143	-0.1138	-0.1519	46.1873	-21.9364	12.9114
16	1.0142	-1.3565	-0.1845	1.6566	-0.7698	8.3154	0.0924	-0.6408	-0.3312	0.4477	0.2039	-0.3281	-0.665	0.0634	-0.2964	0.0269	-0.045	0.2076	0.2105	-0.0556	-0.304	36.8336	-26.7035	20.2481
17	2.0129	1.0619	-1.7188	0.5552	-2.0231	3.6291	0.2235	-0.1042	0.0954	0.1157	0.1185	0.2754	-0.1942	-0.7405	-0.342	-0.3277	-0.065	0.1009	-0.0076	0.0639	-0.2735	30.3989	-44.2461	-6.5045
18	0.542	-2.7134	1.5189	7.7735	-2.4837	1.2425	-0.0275	-0.7434	0.2224	0.3451	0.2025	0.7032	0.3102	-0.4493	-0.1749	-0.2338	-0.073	0.1483	0.2014	0.047	-0.183	24.1549	-40.874	-0.2734
19	4.4873	0.1222	-1.51	4.7319	0.9528	5.4226	0.2141	-0.4185	-0.1398	0.3925	-0.0913	0.1598	-0.0027	-0.4178	-0.1229	-0.125	-0.1262	0.0797	0.0791	0.0936	-0.1838	32.9	-45.768	1.8609
20	4.039	0.6182	-1.711	0.893	2.3728	0.5986	-0.0619	-0.2319	-0.2211	0.1352	-0.0382	0.299	-0.1992	-0.7435	0.1001	-0.1665	-0.1921	0.0249	-0.0508	0.0815	-0.1287	31.173	-48.8833	-9.8948
21	8.4593	0.0802	0.2127	4.4685	3.2312	0	-0.1916	0.0689	0.0818	-0.08	0.3926	0.4425	0.6063	0.0383	-0.201	-0.2821	-0.0434	-0.2076	0.119	0.0556	0.1667	35.0511	-36.9215	-53.6409

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{H\|34 - 52}	H	34 - 52
2	X-RAY DIFFRACTION	2	{H\|53 - 109}	H	53 - 109
3	X-RAY DIFFRACTION	3	{H\|110 - 170}	H	110 - 170
4	X-RAY DIFFRACTION	4	{H\|171 - 182}	H	171 - 182
5	X-RAY DIFFRACTION	5	{H\|183 - 196}	H	183 - 196
6	X-RAY DIFFRACTION	6	{H\|197 - 226}	H	197 - 226
7	X-RAY DIFFRACTION	7	{H\|227 - 247}	H	227 - 247
8	X-RAY DIFFRACTION	8	{H\|248 - 252}	H	248 - 252
9	X-RAY DIFFRACTION	9	{H\|253 - 265}	H	253 - 265
10	X-RAY DIFFRACTION	10	{H\|266 - 280}	H	266 - 280
11	X-RAY DIFFRACTION	11	{H\|281 - 325}	H	281 - 325
12	X-RAY DIFFRACTION	12	{H\|326 - 332}	H	326 - 332
13	X-RAY DIFFRACTION	13	{H\|333 - 359}	H	333 - 359
14	X-RAY DIFFRACTION	14	{H\|360 - 382}	H	360 - 382
15	X-RAY DIFFRACTION	15	{H\|383 - 398}	H	383 - 398
16	X-RAY DIFFRACTION	16	{H\|399 - 408}	H	399 - 408
17	X-RAY DIFFRACTION	17	{H\|409 - 427}	H	409 - 427
18	X-RAY DIFFRACTION	18	{H\|428 - 433}	H	428 - 433
19	X-RAY DIFFRACTION	19	{H\|434 - 493}	H	434 - 493
20	X-RAY DIFFRACTION	20	{H\|494 - 513}	H	494 - 513
21	X-RAY DIFFRACTION	21	{H\|518 - 522}	H	518 - 522

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi