PDB-2y5t: Crystal structure of the pathogenic autoantibody CIIC1 in complex...

ID or keywords:

Entry

Database: PDB / ID: 2y5t

Title

Crystal structure of the pathogenic autoantibody CIIC1 in complex with the triple-helical C1 peptide

Components

(C1) x 2
(CIIC1 FAB FRAGMENT ...) x 2

Keywords

IMMUNE SYSTEM / ANTIBODY / RHEUMATOID ARTHRITIS / ARTHRITOGENIC

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

MUS MUSCULUS (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Dobritzsch, D. / Lindh, I. / Schneider, N. / Uysal, H. / Nandakumar, K.S. / Burkhardt, H. / Schneider, G. / Holmdahl, R.

Citation

Journal: Arthritis Rheum. / Year: 2011
Title: Crystal Structure of an Arthritogenic Anticollagen Immune Complex.
Authors: Dobritzsch, D. / Lindh, I. / Uysal, H. / Nandakumar, K.S. / Burkhardt, H. / Schneider, G. / Holmdahl, R.

History

Deposition	Jan 17, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 14, 2011	Provider: repository / Type: Initial release
Revision 1.1	Aug 23, 2017	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2y5t.cif.gz	216.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2y5t.ent.gz	176 KB	Display	PDB format
PDBx/mmJSON format	2y5t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2y5t_validation.pdf.gz	473.7 KB	Display	wwPDB validaton report
Full document	2y5t_full_validation.pdf.gz	476.2 KB	Display
Data in XML	2y5t_validation.xml.gz	23.4 KB	Display
Data in CIF	2y5t_validation.cif.gz	34 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y5/2y5t ftp://data.pdbj.org/pub/pdb/validation_reports/y5/2y5t	HTTPS FTP

-
Related structure data

Related structure data	2vl5S S: Starting model for refinement
Similar structure data	5xt4-d 5xry-d 2a88-1 4c61-d 5c1w-d 6h0n-d 2xa4-d 5xvt-d 2c5e-d 5xu2-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: CIIC1 FAB FRAGMENT HEAVY CHAIN

B: CIIC1 FAB FRAGMENT LIGHT CHAIN

E: C1

F: C1

G: C1

hetero molecules

58.9 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	81.050, 81.050, 168.450
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

-
Protein/peptide , 2 types, 3 molecules EGF

#3: Protein/peptide	C1 Mass: 3073.250 Da / Num. of mol.: 2 / Fragment: C1-EPITOPE / Source method: obtained synthetically Details: TRIPLE-HELICAL SYNTHETIC PEPTIDE, CHAINS CROSSLINKED AT C-TERMINUS, CONTAINS C1-EPITOPE OF COLLAGEN TYPE II FROM MOUSE FLANKED BY GPO REPEATS Source: (synth.) MUS MUSCULUS (house mouse)
#4: Protein/peptide	C1 Mass: 3551.835 Da / Num. of mol.: 1 / Fragment: C1-EPITOPE / Source method: obtained synthetically Details: TRIPLE-HELICAL SYNTHETIC PEPTIDE, CHAINS CROSSLINKED AT C-TERMINUS, CONTAINS C1-EPITOPE OF COLLAGEN TYPE II FROM MOUSE FLANKED BY GPO REPEATS Source: (synth.) MUS MUSCULUS (house mouse)

-
Antibody , 2 types, 2 molecules AB

#1: Antibody	CIIC1 FAB FRAGMENT HEAVY CHAIN Mass: 24894.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: DISULFIDE BRIDGE BETWEEN A22 AND A96, A146 AND A201, A134 AND A218 A22 AND A96, A146 AND A201, A134 AND A218 Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MURINE HYBRIDOMA
#2: Antibody	CIIC1 FAB FRAGMENT LIGHT CHAIN Mass: 24059.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: DISULFIDE BRIDGE BETWEEN B23 AND B92, B138 AND B198 Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MURINE HYBRIDOMA

-
Non-polymers , 3 types, 296 molecules

#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Nonpolymer details	L-HYDROXYPROLINE (HYP): PEPTIDE-BONDED TO OTHER AMINO ACIDS.

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.7 Å³/Da / Density % sol: 54 % / Description: NONE
Crystal grow	pH: 8 Details: 100 MM TRIS PH 8.0, 55-57% (V/V) 2-METHYL-2,4-PENTANEDIOL.

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.2→56.2 Å / Num. obs: 33244 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / B_iso Wilson estimate: 38.5 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 11.5
Reflection shell	Resolution: 2.2→2.32 Å / Redundancy: 5.4 % / R_merge(I) obs: 0.63 / Mean I/σ(I) obs: 2 / % possible all: 100

-
Processing

Software

Name	Version	Classification
REFMAC	5.4.0078	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VL5

2vl5

Resolution: 2.2→43.85 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.925 / SU B: 12.386 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES A223-233, E1-5, E32-34, F1-5, F33-38, G1-3, G28-34 ARE DISORDERED AND NOT VISIBLE IN THE MAP

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24544	1683	5.1 %	RANDOM
R_work	0.18845	-	-	-
obs	0.19127	31559	99.84 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 16.984 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.17 Å²	0.59 Å²	0 Å²
2-	-	1.17 Å²	0 Å²
3-	-	-	-1.76 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→43.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3860	0	13	293	4166

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	4062
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.27	2.004	5580
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.087	5	538
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.38	24.094	149
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.95	15	601
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.103	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	619
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.022	3131
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.49	1.5	2622
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.93	2	4268
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.419	3	1440
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.231	4.5	1299
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.319	119	-
R_work	0.253	2298	-
obs	-	-	100 %

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	0.8262	-0.2598	-0.521	4.3418	1.1463	1.7144	-0.021	0.106	0.0855	-0.2879	-0.0206	-0.3908	0.0412	0.3066	0.0416	0.2387	-0.0952	-0.047	0.1781	0.0013	0.1952	-26.2297	5.144	12.0717
2	1.46	1.502	0.5186	2.7457	-0.0274	4.7967	-0.0077	-0.2137	-0.0001	-0.0032	-0.0292	0.1623	0.0471	-0.1462	0.0369	0.2145	-0.1136	-0.0789	0.0605	0.0491	0.1732	-37.0253	2.5988	14.895
3	3.2208	0.1111	1.0697	2.5036	0.2043	1.4625	-0.1273	0.1493	-0.0505	-0.2192	0.0516	0.0736	0.1387	-0.0256	0.0757	0.3074	-0.1135	-0.0848	0.1655	0.0426	0.1338	-35.4695	5.9406	5.9597
4	0.2111	0.4329	0.0352	8.5565	0.8152	1.2993	-0.0824	-0.0729	-0.1154	0.1709	0.0264	-0.0788	0.0934	0.1273	0.056	0.2162	-0.0961	-0.0362	0.1136	0.0448	0.1329	-31.9714	-0.1521	18.0397
5	2.298	0.8248	1.5933	1.4096	0.4236	4.3422	-0.169	-0.2286	0.1336	0.0873	-0.0245	0.0479	-0.153	0.0766	0.1935	0.0933	0.0296	0.0237	0.132	-0.0466	0.1882	-22.176	23.4696	36.4745
6	2.6572	0.6789	1.0062	1.3573	-0.2556	3.9914	-0.0362	-0.2232	-0.0063	0.0366	-0.0106	-0.0639	0.2845	0.0264	0.0467	0.16	-0.0016	0.0105	0.1212	-0.0331	0.1291	-18.6193	17.6317	37.1764
7	1.062	0.4781	1.1299	1.4839	0.8067	3.8921	0.0643	-0.3031	0.0076	0.2799	-0.025	0.2905	0.1607	-0.5015	-0.0394	0.313	-0.1286	0.0233	0.2576	0.0296	0.3093	-46.3308	-9.1514	28.2341
8	1.5219	0.5783	0.8883	2.6325	0.4265	3.4391	0.1043	-0.2376	-0.1558	0.3594	-0.0419	0.0497	0.2145	0.0166	-0.0624	0.2768	-0.0837	-0.0201	0.1584	0.0405	0.1749	-38.0667	-7.4793	29.7533
9	0.9156	-0.0804	0.1652	3.0226	0.0225	1.8587	-0.065	-0.1584	0.0775	0.039	-0.003	0.1607	0.2839	-0.366	0.068	0.1117	-0.0562	-0.0139	0.3106	-0.0788	0.1402	-29.5384	23.0224	47.5394
10	0.9672	0.4511	0.736	8.1522	-1.1256	2.4309	0.1062	-0.096	0.0954	0.5264	-0.3011	0.2729	0.2215	-0.3765	0.195	0.2055	-0.1087	0.0256	0.3551	-0.0406	0.1935	-33.3118	16.1164	42.9381
11	2.2979	0.5249	-0.24	1.4778	0.2101	3.3414	-0.0526	-0.0975	0.1023	0.1361	-0.0134	0.1179	-0.0458	-0.2781	0.066	0.1077	0.0193	0.0014	0.3064	-0.1027	0.1627	-30.4982	29.3327	50.0461
12	8.9885	-3.3332	4.2384	4.6737	0.8406	4.4146	-0.2094	-0.7009	0.6907	0.4743	-0.1774	-0.822	-0.8617	0.4311	0.3867	0.2234	-0.0419	0.0451	0.3399	-0.0633	0.2099	-19.7518	34.836	53.1291
13	7.0172	-4.5231	0.9031	4.4156	-0.7179	0.1285	0.8556	-0.9296	-0.7961	-1.2025	-0.2186	0.2861	-0.6097	1.2664	-0.637	0.4639	0.0439	0.0729	0.5343	0.0013	0.5228	-13.942	-25.0331	8.2983
14	6.7667	-0.8852	4.2158	3.6577	-0.6316	6.3106	-0.196	0.3772	-0.4738	-0.1524	0.1164	0.3067	0.0758	0.1016	0.0796	0.4118	-0.1379	0.0008	0.0809	0.0044	0.1902	-39.1099	-11.7509	5.5796
15	2.3791	0.9406	-3.4677	0.6759	-0.403	8.1364	1.3052	0.0291	-0.8443	-0.543	-0.7032	0.5871	-0.4726	-0.8378	-0.602	0.6207	-0.0587	0.0107	0.5783	0.1017	0.7366	-61.9692	-7.1734	1.7811
16	0.6121	0.7116	0.2203	0.8272	0.2561	0.0793	0.7761	-0.0228	-0.3574	-0.5793	-0.5088	-0.651	0.418	0.3105	-0.2673	0.5622	-0.0108	0.0413	0.6188	0.0409	0.5896	-12.6212	-22.3254	8.5203
17	7.8787	-1.1043	3.2837	3.7421	2.6128	4.8473	-0.7146	0.8007	-0.6594	-0.3825	0.4192	-0.0124	0.2874	0.0843	0.2954	0.4254	-0.0931	-0.0393	0.1278	0.0108	0.1648	-39.7923	-15.2212	4.2929
18	10.1465	-3.7159	-0.8104	1.3609	0.2968	0.0647	0.3765	-0.354	0.4482	-0.1492	-0.0066	0.1933	0.0948	-0.1567	-0.3699	0.3846	-0.0482	-0.0211	0.3793	-0.0168	0.4666	-61.2149	-7.6989	6.991
19	10.1569	-4.6867	-0.1255	2.1651	0.0511	0.0206	0.4989	0.1847	0.5031	-0.1559	-0.2629	-0.2772	0.0197	0.268	-0.236	0.4022	0.0154	0.0195	0.3607	-0.015	0.3699	-13.305	-23.0494	5.5199
20	1.6908	2.1561	-0.2359	3.0546	-1.3105	3.3738	-0.2166	-0.2002	-0.6923	-0.3457	0.1313	0.3475	0.3945	0.0522	0.0853	0.3684	-0.1202	-0.0798	0.159	-0.0362	0.1839	-39.3492	-15.0046	8.4159
21	8.3681	-1.1405	4.6088	0.6809	-2.1889	7.1739	0.1208	0.3035	0.6124	0.1427	0.0393	0.1424	-0.4488	-0.7594	-0.1601	0.5135	-0.0349	-0.0023	0.4083	0.0099	0.4817	-54.4398	-4.7261	6.3432

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 33
2	X-RAY DIFFRACTION	2	A	34 - 54
3	X-RAY DIFFRACTION	3	A	55 - 88
4	X-RAY DIFFRACTION	4	A	89 - 115
5	X-RAY DIFFRACTION	5	A	116 - 153
6	X-RAY DIFFRACTION	6	A	154 - 222
7	X-RAY DIFFRACTION	7	B	1 - 37
8	X-RAY DIFFRACTION	8	B	38 - 111
9	X-RAY DIFFRACTION	9	B	112 - 158
10	X-RAY DIFFRACTION	10	B	159 - 179
11	X-RAY DIFFRACTION	11	B	180 - 212
12	X-RAY DIFFRACTION	12	B	213 - 218
13	X-RAY DIFFRACTION	13	E	5 - 14
14	X-RAY DIFFRACTION	14	E	15 - 24
15	X-RAY DIFFRACTION	15	E	25 - 31
16	X-RAY DIFFRACTION	16	F	4 - 16
17	X-RAY DIFFRACTION	17	F	17 - 24
18	X-RAY DIFFRACTION	18	F	25 - 32
19	X-RAY DIFFRACTION	19	G	3 - 14
20	X-RAY DIFFRACTION	20	G	15 - 22
21	X-RAY DIFFRACTION	21	G	23 - 29

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein/peptide , 2 types, 3 molecules EGF

-
Antibody , 2 types, 2 molecules AB

-
Non-polymers , 3 types, 296 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein/peptide , 2 types, 3 molecules EGF

-Antibody , 2 types, 2 molecules AB

-Non-polymers , 3 types, 296 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein/peptide , 2 types, 3 molecules EGF

-
Antibody , 2 types, 2 molecules AB

-
Non-polymers , 3 types, 296 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi