PDB-7mrk: Chicken CNTN4 APP complex

ID or keywords:

Entry

Database: PDB / ID: 7mrk

Title

Chicken CNTN4 APP complex

Components

Amyloid-beta A4 protein
Contactin-4

Keywords

CELL ADHESION / Ig superfamily / amyloid precursor protein

Function / homology

Function and homology information

positive regulation of macromolecule metabolic process / secretory vesicle / regulation of protein metabolic process / Golgi-associated vesicle / transition metal ion binding / clathrin-coated pit / axon guidance / molecular function activator activity / serine-type endopeptidase inhibitor activity / endocytosis ...
Similarity search - Function

Basigin-like / Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal ...
Similarity search - Domain/homology

Biological species

Gallus gallus (chicken)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Bouyain, S. / Karuppan, S.J.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2021
Title: Members of the vertebrate contactin and amyloid precursor protein families interact through a conserved interface.
Authors: Karuppan, S.J. / Vogt, A. / Fischer, Z. / Ladutska, A. / Swiastyn, J. / McGraw, H.F. / Bouyain, S.

History

Deposition	May 7, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 5, 2022	Provider: repository / Type: Initial release
Revision 1.1	Feb 9, 2022	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7mrk.cif.gz	415.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7mrk.ent.gz	281.9 KB	Display	PDB format
PDBx/mmJSON format	7mrk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7mrk_validation.pdf.gz	455.6 KB	Display	wwPDB validaton report
Full document	7mrk_full_validation.pdf.gz	458.4 KB	Display
Data in XML	7mrk_validation.xml.gz	34.1 KB	Display
Data in CIF	7mrk_validation.cif.gz	49.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mr/7mrk ftp://data.pdbj.org/pub/pdb/validation_reports/mr/7mrk	HTTPS FTP

-
Related structure data

Related structure data	7mqyC 7mrmC 7mrnC 7mroC 7mrqC 7mrsC 3ktmS 5e4sS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2hsz-d 6gbh-2 6krz-1 6gbh-1 6gbg-d 1fgk-d 6jbz-d 2yg8-d 4f64-d 1fgi-d Search similar-shape structures by Omokage search (details) 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#79 - Jul 2006 Amyloid-beta Precursor Protein similarity (30) #189 - Sep 2015 Amyloids similarity (30) #46 - Oct 2003 Trypsin similarity (7) #185 - May 2015 Titin similarity (3) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (2) #52 - Apr 2004 Growth Hormone similarity (1) #142 - Oct 2011 PDB Pioneers similarity (7) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#79 - Jul 2006
Amyloid-beta Precursor Protein
similarity (30)
#189 - Sep 2015
Amyloids
similarity (30)
#46 - Oct 2003
Trypsin
similarity (7)
#185 - May 2015
Titin
similarity (3)
#267 - Mar 2022
Vascular Endothelial Growth Factor (VegF
similarity (2)
#52 - Apr 2004
Growth Hormone
similarity (1)
#142 - Oct 2011
PDB Pioneers
similarity (7)
#141 - Sep 2011
O-GlcNAc Transferase
similarity (1)

Deposited unit

A: Amyloid-beta A4 protein

B: Contactin-4

C: Amyloid-beta A4 protein

D: Contactin-4

hetero molecules

108 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Amyloid-beta A4 protein

B: Contactin-4

hetero molecules

defined by author&software
Evidence: surface plasmon resonance
54.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Amyloid-beta A4 protein

D: Contactin-4

defined by author&software
54.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	128.450, 65.510, 158.294
Angle α, β, γ (deg.)	90.000, 92.919, 90.000
Int Tables number	5
Space group name H-M	I121
Space group name Hall	C2y(x,y,-x+z)
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z+1/2 #4: -x+1/2,y+1/2,-z+1/2

#1: Protein	Amyloid-beta A4 protein Mass: 20582.480 Da / Num. of mol.: 2 / Fragment: E1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DGJ7
#2: Protein	Contactin-4 / CNTN4 Mass: 33558.238 Da / Num. of mol.: 2 / Fragment: domains FN1-FN3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: CNTN4 / Production host: Escherichia coli (E. coli) / References: UniProt: F1P3U6
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.07 Å³/Da / Density % sol: 59.95 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 150 mM (NH4)2SO4, 50 mM Na-cacodylate pH 6.5, 30% (v/v) PEG 550 MME

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 10, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.05→64.14 Å / Num. obs: 82428 / % possible obs: 99.7 % / Redundancy: 6.4 % / B_iso Wilson estimate: 35.78 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.101 / R_pim(I) all: 0.044 / R_rim(I) all: 0.111 / Net I/σ(I): 10
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.772 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4511 / CC_1/2: 0.805 / R_pim(I) all: 0.326 / R_rim(I) all: 0.839 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KTM, 5E4S

3ktm

5e4s

Resolution: 2.05→32.41 Å / SU ML: 0.2393 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.7305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2248	1938	2.42 %
R_work	0.1834	78072	-
obs	0.1844	80010	96.74 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 49.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→32.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6322	0	7	508	6837

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0031	6493
X-RAY DIFFRACTION	f_angle_d	0.5905	8853
X-RAY DIFFRACTION	f_chiral_restr	0.0483	979
X-RAY DIFFRACTION	f_plane_restr	0.004	1152
X-RAY DIFFRACTION	f_dihedral_angle_d	12.2585	2367

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.05-2.1	0.3233	126	0.2545	5186	X-RAY DIFFRACTION	90.99
2.1-2.16	0.2421	131	0.2228	5319	X-RAY DIFFRACTION	92.94
2.16-2.22	0.2415	132	0.2062	5389	X-RAY DIFFRACTION	94.02
2.22-2.29	0.243	150	0.2033	5400	X-RAY DIFFRACTION	94.63
2.29-2.38	0.2253	119	0.1969	5564	X-RAY DIFFRACTION	96.24
2.38-2.47	0.2597	137	0.205	5513	X-RAY DIFFRACTION	96.47
2.47-2.58	0.2512	149	0.2083	5586	X-RAY DIFFRACTION	97.47
2.58-2.72	0.244	138	0.2132	5660	X-RAY DIFFRACTION	98.29
2.72-2.89	0.2481	141	0.2135	5663	X-RAY DIFFRACTION	98.72
2.89-3.11	0.2564	141	0.2063	5778	X-RAY DIFFRACTION	99.51
3.11-3.42	0.2337	145	0.1881	5745	X-RAY DIFFRACTION	99.8
3.42-3.92	0.2295	145	0.1701	5753	X-RAY DIFFRACTION	99.76
3.92-4.94	0.1896	144	0.1455	5819	X-RAY DIFFRACTION	99.62
4.94-32.41	0.1865	140	0.166	5697	X-RAY DIFFRACTION	95.83

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	7.01375134696	4.0323751577	2.72408779196	2.94092332214	0.939584976917	2.35060984815	-0.435551790275	0.0540059774758	0.430031087945	-0.309911033404	0.430627646039	0.666361278428	-0.664026211278	-0.288794911632	-0.0877546319888	0.501780753047	0.0813094731997	-0.000429920659493	0.3575452758	-0.00619331792692	0.451214746508	13.8350629894	85.7932961279	56.8389484253
2	5.89300803222	0.449308904367	-1.43309460924	9.02388625593	-0.256393353806	5.56073445932	-0.29594689445	-0.464404582359	0.893895484342	0.221480037004	0.380803517353	0.59714283335	-0.993984343741	-0.431153485269	-0.059156612101	0.5317598832	0.0297243290838	-0.0411118980694	0.31426228249	-0.111781660212	0.520914316521	16.1866614785	89.2022160167	60.2417183292
3	2.79636029375	2.02665077185	2.57588985529	2.9126487315	3.21077801418	3.70218702677	0.0229307820518	0.327121127611	1.12657653055	-0.88667984224	0.218235239681	-0.073853515527	-1.20560716464	0.765256051646	0.00270279572574	0.653351855712	-0.0522282403692	-0.0086321401276	0.359688301349	-0.0469375181539	0.480575501819	23.3989475309	88.2718631779	52.315951335
4	3.43231581422	0.815189368359	0.248731173192	5.79779069647	0.716135429806	2.49659001625	-0.141017503518	-0.221763344205	0.119215816009	0.0875195464294	0.119788489679	-0.0997982962507	-0.427439197849	0.0877292312755	-0.0198114687215	0.389337388108	-0.0253340176517	0.0504461112639	0.327099148738	-0.104586458928	0.327974180268	21.2990249671	80.7349287043	57.6103923605
5	5.56744154961	-0.158690173832	0.282496884111	2.15297392269	-0.259016756584	6.94849003186	-0.172396344599	0.315473056507	2.07435924086	1.14943400518	-0.51751135735	1.83795464136	-1.69045219522	-0.708270145793	-0.20938261561	0.769377240312	0.133363909742	0.0339101644187	0.720811627186	-0.149968968227	1.09212433984	5.99185012457	93.5413674473	60.5564861356
6	2.23745761332	0.0585562635856	-0.0414433754122	4.98996593122	0.00281709436074	5.09483730825	-0.101335908642	-0.542470150784	1.08303275932	-0.0505216479851	0.191927303276	0.456999711761	-0.480324793177	-0.253240363277	-0.0208315941535	0.364301654765	0.0292287944251	0.00218504691903	0.267077860052	-0.067054064591	0.351539564707	16.4136114689	79.76128012	56.1270251478
7	3.73677799758	3.92745994382	-2.04543258595	4.25380891922	-2.74339248553	6.01828632228	-0.265374860706	-0.710511788014	-0.427285638918	-0.344907512548	-0.0555290214484	-0.743959356781	0.38517260107	0.609930181537	0.15488556744	0.335950657055	0.019553303152	0.0335818532191	0.362488563952	-0.0864146295368	0.347131585447	25.176432583	63.6045003712	59.6644447856
8	2.80497359569	-2.20117376542	0.494857977884	6.09746955411	-3.23374250083	8.63200915872	0.230770886388	0.623004141543	-0.156650717035	-1.0132397734	-0.448343805736	-0.278867998717	0.274182716611	0.438200140475	0.263471715884	0.406759586412	0.0362076453612	-0.00683620408187	0.470594656143	-0.149798701475	0.289559166976	26.6681021473	63.489202687	45.2801200713
9	2.78452266427	2.24283006807	-1.4949504034	8.51894717095	-4.6664512684	3.16260482749	0.0446816166641	0.423187298737	-0.637080615417	-0.552675547268	0.141321384516	0.341401212585	0.369041336852	-0.36001393332	-0.141083752637	0.303394442426	-0.0391400919137	-0.0718288533969	0.352430470205	-0.130543920943	0.354649397683	16.8766884841	62.1986643437	46.4431526642
10	3.4089694932	1.31939909847	0.443935485001	8.03866054009	-0.852929100934	3.9921782443	0.243777218353	0.0672670238575	-0.329426760741	0.114731646035	-0.157205853226	0.338223510854	0.0691821708677	-0.0232423103814	-0.120289932864	0.219377610333	-0.00505975406849	-0.0111211017917	0.272853746502	-0.115445507082	0.24518875523	21.50772314	64.7488864306	51.1851316554
11	7.35274723758	-2.54950725593	-0.947691190199	3.26828851695	1.32053398297	2.40110253768	0.0163479562863	0.174751283623	-0.134259560355	-0.0687121852001	-0.0505966309822	-0.270617205516	0.194737935694	0.0735174993111	-0.00221696011977	0.256768095294	-0.0046678892699	0.0744862814003	0.205103082321	-0.00337088005395	0.313396807589	61.8192159507	39.9367493535	36.2618794609
12	8.12300522943	-3.11361681207	-2.93886577617	3.44769591317	1.35564981177	2.76394258805	0.0727349193741	0.0795902621321	0.565307836545	-0.0936618830709	0.0937044287876	-0.378201744616	0.00704295335525	-0.0676513423854	-0.074913487061	0.213569169766	-0.00768641215993	0.0193135270563	0.208977395705	-0.0328681321231	0.295685839629	57.7855175922	45.6826362616	38.4170653131
13	2.51242392258	-0.812435730865	-0.9862359353	2.94335764345	0.962776596895	4.98214182914	0.00162440187899	-0.621696403016	0.421652873903	0.491622478191	0.225955782541	-0.506803519451	0.072497759258	0.379862537659	-0.182573576762	0.304339563657	0.0500731271378	-0.0705083895152	0.419796967546	-0.108563152265	0.284777213113	37.0105816817	60.2250285117	61.0583768222
14	3.22137146943	-0.355662186365	-0.561926997754	2.0566548313	-0.410255823107	1.20495525293	-0.210617806399	-0.72642313757	0.524598263845	0.815808137428	0.0722649170796	-0.0198295996156	-0.314010620828	0.493649943323	0.0828679115529	0.507351323446	0.0407535819798	-0.063318330204	0.532559913587	-0.141979172477	0.28590615502	33.1902012556	61.6806242198	65.7658906872
15	7.97347927187	-0.372511637096	0.875526744851	8.04110546696	0.66930799549	7.11926268359	-0.533881171684	-0.864037748326	-0.972450162686	0.661267980866	0.268926759601	-0.268172249964	0.308177832699	0.221007457201	0.346817444094	0.708207566629	0.248968511457	0.0542319207408	0.505239239676	0.0971116765464	0.541375495826	109.160824029	24.8946979225	62.075099227
16	5.83225178997	-0.465079338544	-0.861983725746	9.12056434509	-4.78215943877	3.56965688939	-0.708386782626	0.481982938661	-1.87113765591	-0.518630808845	0.177931112387	0.439526454811	1.59568698049	0.0707935766624	0.104409198692	0.907879156228	0.0246283730477	0.135301380161	0.339070696671	-0.0566544632219	0.726673372655	104.704605829	20.2565793058	52.7743302929
17	6.14599078422	-0.579686365234	1.51808933444	6.94415636317	-1.33588626728	2.63033918885	0.0353279947191	-0.360133475223	-0.627794432008	0.442615590638	-0.0739713114309	-0.150642132875	0.722754668325	0.433829405324	0.16784067519	0.65722648081	0.150898185948	-0.0161848037936	0.39695130415	0.0053611745742	0.402346084596	108.835956386	25.2462888382	58.8991060151
18	5.63973189105	-4.94286956547	1.03316823973	4.59678163003	-0.655702293881	0.39835930405	-0.282461907763	-0.70213567636	-0.467402319276	0.259655613636	0.172315735465	-0.0778450373239	0.264186043368	0.0602721584541	0.105779117627	0.532354744834	0.157812334571	-0.0151689115089	0.440053823024	0.0110706756417	0.428236018756	107.807265966	30.9838690713	56.5683583353
19	8.19282003638	3.97397507085	0.00234422299059	3.30671677455	3.06360711823	7.171699791	0.188510624978	-0.376718639384	0.0396936168011	0.341216041149	-0.210709552497	0.134317039036	-0.182105226797	-0.0184524085613	0.0387362058065	0.251712535095	0.0336281485383	-0.0646014325891	0.231441701216	0.0828374193632	0.220163447618	99.128909477	47.3076693235	59.9674968527
20	3.83864328902	-2.7435150112	-1.24082052035	4.86003244251	1.86706482296	5.93901793397	0.361797713239	0.814281040195	-0.055181996146	-0.978521754115	-0.413550673459	-0.0135540951082	-0.263327519153	-0.581826059927	0.111071926085	0.380065437191	0.017173846598	-0.020851985431	0.469470181893	0.0759012211626	0.247361548033	97.6952130372	47.2796753289	45.5378725315
21	5.12726327777	1.99233094647	0.382456286974	9.8806430598	5.44782547358	4.67481732285	0.0474124174009	0.45440510407	0.500976555147	-0.359362503912	0.302880830747	-0.300276302801	-0.369018021768	0.616096621307	-0.34282254604	0.320701187155	-0.0148778756403	0.0593233408241	0.378456302274	0.0564865572931	0.271830897854	107.436445412	48.5630149127	46.7400992482
22	4.86495423255	1.87989806921	-0.867064217798	9.60711259776	0.64108622832	4.64800192005	0.194481642932	-0.0179573839057	0.0311767653526	0.127194865352	-0.135078302538	-0.351080205652	0.0761974588314	0.200311561049	-0.0793717179482	0.15446334569	0.0201570814423	-0.0131063069076	0.243665511058	0.0549945822871	0.16390867012	102.756138677	46.0672355623	51.4883756843
23	7.66006966911	-3.09858788404	1.07296852632	2.68139565309	-1.31752545901	1.6056470269	0.080792127518	0.207729988746	0.0504462396461	-0.0658722634614	-0.0229394193327	0.493525162011	-0.216324267237	-0.0783818961726	-0.0554606596735	0.316218094718	-0.00114742041557	-0.102018007129	0.249135812381	0.0654499070838	0.508017001616	63.3656094318	69.6217468815	37.0286487814
24	3.8627838724	0.033193299257	3.7273092224	1.90806428778	-1.62032657868	6.2672545249	-0.251016817339	0.184889562163	-0.000776689291353	0.0811859428785	-0.0349586361194	0.328158439338	-0.0787207326729	0.362633650891	0.308592073888	0.282465033572	0.0862694130136	0.0184313268084	0.244688751816	0.0220225645326	0.374547687689	78.4399961138	58.7871905868	46.715623904
25	2.85958258363	-0.380721755303	-0.0405627636875	3.00550291642	-0.836000629395	4.92883687342	0.051815709246	-0.503952387657	-0.279999650764	0.527998352913	0.115768936806	0.378729497981	0.130323679286	-0.148586822085	-0.232705487801	0.330642069197	0.00636869613861	0.0490700127313	0.314197390469	0.126722052747	0.28140124552	89.495790417	48.4926481187	63.6672277296
26	0.975550115265	0.663996083063	-0.0874098282461	1.98918194265	-4.27312290015	4.57416155006	0.1569772917	-0.345197968463	-0.0751611660439	0.165943763776	-0.110593571478	0.180227832292	0.307393714309	0.375302761954	-0.0361899746303	0.754642829566	0.084462079383	0.10800506472	0.512627117717	0.174128304664	0.293001879542	89.2743418454	45.8982201474	73.5878145549
27	6.1661528948	-1.34747502718	-3.07531911791	1.48140106279	1.59901411479	6.15092058001	-0.0575265349523	0.436096727563	0.0609503341985	-0.303557229885	-0.292596653639	0.397399500093	-0.344120101197	-0.197727870434	0.31088476763	0.51966347725	0.0453836289526	0.0380953325447	0.335824134513	0.0865866749481	0.370731744611	77.4236395249	31.0563953868	99.1037057313

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 30 through 42 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 65 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 66 through 76 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 77 through 94 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 95 through 109 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 110 through 119 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 120 through 133 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 134 through 146 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 147 through 161 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 162 through 189 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 595 through 658 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 659 through 698 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 699 through 759 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 760 through 798 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 30 through 54 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 55 through 76 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 77 through 109 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 110 through 119 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 120 through 133 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 134 through 146 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 147 through 161 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 162 through 189 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 596 through 688 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 689 through 708 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 709 through 781 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 782 through 809 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 810 through 900 )

-
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

-
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

-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

-
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