PDB-7op0: Crystal structure of complement C5 in complex with chemically syn...

ID or keywords:

Entry

Database: PDB / ID: 7op0

Title

Crystal structure of complement C5 in complex with chemically synthesized K92 knob domain.

Components

(Complement C5 ...Complement component 5) x 2
K92chemFE

Keywords

IMMUNE SYSTEM /

Complement C5 / C5 / ultralong / ultra-long / knob domain.

Function / homology

Function and homology information

Terminal pathway of complement /

membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis /

complement activation, alternative pathway /

chemokine activity /

endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production /

complement activation, classical pathway / positive regulation of chemokine production ...
Similarity search - Function

Biological species

Homo sapiens (human)

Bos taurus (cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.57 Å

Authors

Macpherson, A. / van der Elsen, J.M.H. / Schulze, M.E. / Birtley, J.R.

Citation

Journal: Acs Chem.Biol. / Year: 2021
Title: The Chemical Synthesis of Knob Domain Antibody Fragments.
Authors: Macpherson, A. / Birtley, J.R. / Broadbridge, R.J. / Brady, K. / Schulze, M.E.D. / Tang, Y. / Joyce, C. / Saunders, K. / Bogle, G. / Horton, J. / Kelm, S. / Taylor, R.D. / Franklin, R.J. / ...

History

Deposition	May 28, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 6, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7op0.cif.gz	808.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7op0.ent.gz	563.7 KB	Display	PDB format
PDBx/mmJSON format	7op0.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/op/7op0 ftp://data.pdbj.org/pub/pdb/validation_reports/op/7op0	HTTPS FTP

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Related structure data

Related structure data	7ad6S S: Starting model for refinement
Similar structure data	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
Related items in Molecule of the Month	#201 - Sep 2016 Isoprene Synthase similarity (1) #96 - Dec 2007 Oxidosqualene Cyclase similarity (1) #217 - Jan 2018 Opioid Receptors similarity (1) #202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (1) #25 - Jan 2002 Thrombin similarity (1) #149 - May 2012 Leptin similarity (1) #83 - Nov 2006 Fibrin similarity (1)

Deposited unit

A: Complement C5 alpha chain

B: Complement C5 beta chain

C: K92chemFE

hetero molecules

190 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: surface plasmon resonance

Unit cell

Length a, b, c (Å)	204.840, 104.820, 155.060
Angle α, β, γ (deg.)	90.000, 125.130, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

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Complement C5 ... , 2 types, 2 molecules AB

#1: Protein	Complement C5 alpha chain Mass: 112635.008 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C5, CPAMD4 / Production host: Homo sapiens (human) / References: UniProt: P01031
#2: Protein	Complement C5 beta chain Mass: 73615.766 Da / Num. of mol.: 1 / Fragment: beta chain, UNP residues 1-675 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C5, CPAMD4 / Production host: Homo sapiens (human) / References: UniProt: P01031

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Protein/peptide / Sugars , 2 types, 2 molecules C

#3: Protein/peptide

K92chemFE

Mass: 3692.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TCPEGWSECGVAIYGYACGRWGCGHFLNSGPNISP / Source: (synth.)

Bos taurus (cattle)

#4: 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

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Non-polymers , 2 types, 31 molecules

#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.58 Å³/Da / Density % sol: 65.68 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M bicine/Trizma (pH 8.5), 10 % (w/v) PEG 8000, 20 % (v/v) ethylene glycol, 30 mM sodium fluoride, 30 mM sodium bromide, 30 mM sodium iodide.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 13, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.57→57 Å / Num. obs: 85364 / % possible obs: 99 % / Redundancy: 13.4 % / B_iso Wilson estimate: 88.7 Å² / CC_1/2: 0.99 / Net I/σ(I): 17.75
Reflection shell	Resolution: 2.57→2.66 Å / Mean I/σ(I) obs: 2.29 / Num. unique obs: 8497 / CC_1/2: 0.61

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Processing

Software

Name	Version	Classification
REFMAC	5.5	refinement
PHENIX	1.18_3845	refinement
xia2		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7AD6

7ad6

Resolution: 2.57→56.67 Å / SU ML: 0.4439 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.0027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2642	4271	5 %
R_work	0.2312	81093	-
obs	0.2329	85364	99.78 %

Solvent computation

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

Displacement parameters

B_iso mean: 121.97 Å²

Refinement step

Cycle: LAST / Resolution: 2.57→56.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13002	0	36	29	13067

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0027	13319
X-RAY DIFFRACTION	f_angle_d	0.6108	18084
X-RAY DIFFRACTION	f_chiral_restr	0.0443	2067
X-RAY DIFFRACTION	f_plane_restr	0.0038	2301
X-RAY DIFFRACTION	f_dihedral_angle_d	18.0452	4856

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 (%)
2.57-2.6	0.4161	131	0.3728	2746	X-RAY DIFFRACTION	99.83
2.6-2.63	0.4448	138	0.3783	2666	X-RAY DIFFRACTION	99.72
2.63-2.66	0.3597	147	0.3598	2669	X-RAY DIFFRACTION	99.68
2.66-2.7	0.3548	151	0.3585	2662	X-RAY DIFFRACTION	99.86
2.7-2.73	0.4217	151	0.3448	2699	X-RAY DIFFRACTION	99.86
2.73-2.77	0.3643	147	0.345	2674	X-RAY DIFFRACTION	99.86
2.77-2.81	0.3573	145	0.3411	2719	X-RAY DIFFRACTION	99.86
2.81-2.85	0.4019	146	0.3478	2654	X-RAY DIFFRACTION	99.79
2.85-2.89	0.3604	145	0.3433	2696	X-RAY DIFFRACTION	99.82
2.89-2.94	0.4123	139	0.3439	2695	X-RAY DIFFRACTION	99.96
2.94-2.99	0.3802	140	0.3351	2700	X-RAY DIFFRACTION	99.72
2.99-3.05	0.3635	140	0.3353	2677	X-RAY DIFFRACTION	99.89
3.05-3.11	0.3877	136	0.3108	2728	X-RAY DIFFRACTION	99.9
3.11-3.17	0.3554	116	0.3101	2701	X-RAY DIFFRACTION	99.89
3.17-3.24	0.3571	157	0.3053	2705	X-RAY DIFFRACTION	99.86
3.24-3.31	0.3326	139	0.2949	2678	X-RAY DIFFRACTION	99.86
3.31-3.4	0.3057	152	0.2948	2694	X-RAY DIFFRACTION	99.89
3.4-3.49	0.3048	130	0.2821	2716	X-RAY DIFFRACTION	99.86
3.49-3.59	0.2901	160	0.2646	2699	X-RAY DIFFRACTION	99.93
3.59-3.71	0.2665	152	0.2604	2692	X-RAY DIFFRACTION	99.75
3.71-3.84	0.3062	142	0.2545	2697	X-RAY DIFFRACTION	99.82
3.84-3.99	0.3029	148	0.2369	2676	X-RAY DIFFRACTION	99.54
3.99-4.17	0.2488	140	0.2259	2719	X-RAY DIFFRACTION	99.93
4.17-4.39	0.2204	134	0.2004	2703	X-RAY DIFFRACTION	99.79
4.39-4.67	0.2291	141	0.1907	2719	X-RAY DIFFRACTION	99.69
4.67-5.03	0.2155	131	0.1722	2728	X-RAY DIFFRACTION	99.79
5.03-5.53	0.2354	140	0.1868	2742	X-RAY DIFFRACTION	99.97
5.54-6.34	0.2611	139	0.2185	2723	X-RAY DIFFRACTION	100
6.34-7.98	0.2355	151	0.2244	2738	X-RAY DIFFRACTION	99.93
7.98-56.67	0.1986	143	0.1771	2778	X-RAY DIFFRACTION	98.45

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	0.677130727928	0.146174704725	0.392207089002	0.378970304354	0.0880927918562	2.02202457885	0.0270969267693	-0.356156857654	-0.0432711831815	-0.0825189857758	0.0902450284853	0.227837155416	-0.120815871636	-0.747079775615	-0.122738906757	0.669763184358	-0.0144956639517	-0.0572576967344	1.02758847184	0.282501145619	1.05258996378	-39.5201904752	-51.5384090072	34.1354037218
2	2.31525893529	0.309428935014	-0.265492033106	1.45494721534	-0.469757510098	1.61302187851	-0.105361301403	0.0535146065906	0.0139720024263	-0.155026017898	0.15708184663	0.0488805125359	-0.275176586568	0.0714155598246	-0.0285800137911	0.796214491894	-0.160340430973	-0.0771914092264	0.668357813348	0.0360055173685	0.627484833987	-8.70018654774	-35.9681695681	36.2372898413
3	0.2647619049	-1.50377980061	0.922270461188	4.97915030671	-3.92513544804	4.73730791981	-0.294232213903	-0.188058974857	-0.353077096468	0.488035725813	0.234837918271	0.257357544327	-0.0274965899068	0.0762164028859	0.00435059176948	0.756014609667	0.136712493344	0.135595629632	0.987945937454	0.24058142449	1.04290134932	-19.9766866997	-58.6440915731	71.0486647083
4	2.60954638875	0.207279590689	-0.347179173955	2.45883934365	-1.6618770769	5.26988740404	0.44748141119	0.54582145682	-0.507433918979	-0.481602360659	-0.438344209636	-0.103772201795	-0.130533988141	0.0152148856473	-0.0164466657939	0.72525486417	0.305240772897	-0.0964593543024	0.805157001846	-0.109374513361	0.668557425406	-29.743100369	-39.9607260523	-29.3523225835
5	2.94578092248	-0.573905752476	-0.925085972764	1.85336479536	0.221235231921	3.13785624006	-0.0657873741367	-0.247959663189	-0.219523105347	0.323877547829	0.0643541246638	0.124652367577	-0.0173582715091	0.0716163105153	-0.01784556368	0.827509924607	-0.0429126757517	-0.073189065121	0.709702571844	0.065530659895	0.797524988464	-34.6913061967	-44.5272021062	9.38703877138
6	2.16770707707	0.583864854047	-1.87322408716	1.88774419025	-0.608966986255	5.17621471263	0.373018752793	0.023723259786	-0.325131905723	1.03590400053	-0.235166768938	-0.170687963705	-1.68775103151	-0.581056535649	-0.197380575081	1.35009206315	0.151819650553	-0.00813446463612	1.41159596835	0.096286535222	1.16114131244	-61.4998167564	-38.29414063	23.4252781703
7	0.954470244499	0.348321388631	-0.959397541348	0.499390711262	-0.620796149067	3.95956598478	0.0345970780503	0.594206212301	-0.525513817436	0.0418476156773	-0.135841380069	0.483274315349	-0.673507341442	-2.10585482816	-0.0934824927888	0.986093981367	0.350718140892	-0.0674427683192	2.18119788124	-0.115481823187	1.39257787798	-65.0383691551	-40.9823456589	-6.43183684016
8	0.201492762906	-0.454056676366	-0.212762125892	0.976123045607	-0.0426530667675	1.74834477418	0.0491530328434	0.528640088885	-0.494538257233	0.00564994140812	-0.135743591882	0.662254373739	-0.0689165155436	-1.38021475804	0.0353536523696	0.92216002339	0.256939734988	-0.195805341356	2.05114484231	-0.222777598077	1.33354345356	-61.6710603098	-45.3712305534	-20.5074375702
9	0.986891847851	-0.297957103116	0.976031876209	2.14186139149	-2.0283068397	7.00079271918	0.0725572097386	0.15721336294	-0.526219170253	-0.241327001567	-0.0330174567833	0.395236926235	0.124542874288	-1.33364450089	-0.117593657628	0.745344284886	0.0408281362187	-0.233690776027	1.23956499519	-0.243015919205	1.08678689554	-46.9873772998	-53.1457177748	-23.6694571872
10	0.86744574699	0.405057622933	-1.18646930863	0.345121244627	-0.103704924348	5.62614533588	0.173533087295	0.401206253648	0.0241571750838	-0.357292051397	0.321137384803	0.526617132234	0.690377054188	-1.06674037627	-0.3296833657	1.1061810761	-0.11510953132	-0.199221419537	1.03577980481	0.0536831938183	1.40634698043	-37.4194466974	-57.0919707992	0.87680038812
11	6.21715227909	-0.939256880478	-4.35016858543	1.6815530242	1.40578267231	7.09755262477	0.371631908317	-0.280962290698	0.143287117361	0.0782233135248	-0.376898707425	-0.173162373253	-1.22822409815	-1.05828005201	-0.19365817189	1.08053732156	0.414705637576	-0.320968653652	1.44928883103	-0.292646752347	0.996687849781	-45.5928749418	-34.2943758545	-24.8131524996
12	5.80833937666	-4.73950068136	-5.27288006967	5.60406934193	5.51355394442	6.60923353191	0.0972888056762	0.640415111526	1.36893005622	-0.775915156804	-0.255259855441	2.89018194259	2.36504737617	2.68361350566	0.0867713872363	2.65639489232	0.803227198742	-0.614652881221	2.08832246145	-0.0134102508561	1.80716658522	-21.8848220612	-61.3889951738	-32.242225484
13	2.56723454784	-1.68900858128	1.04059980236	7.86740900636	4.05239150509	3.78054353265	0.551390815892	0.739316258545	-1.075909497	0.403169585853	-0.725697730661	-2.27197392885	1.33971474431	0.734103483097	-0.0355834868941	1.36761225227	0.179887390339	0.154158537326	1.7700748616	0.366235009569	2.52644426814	-30.2725658125	-57.1373636397	-26.2804806347
14	0.279481645534	0.178943491529	0.540226466094	1.99537134726	-2.50799351736	5.49933549143	0.68657591636	0.747521805536	-0.111142720716	-0.607166522857	-0.733664313207	0.485539596851	0.454491779054	0.240677036148	0.0349501412389	1.5888865553	0.532913153703	-0.103990897793	1.53775004035	0.152631254164	3.65046729666	-30.3816883534	-59.5860232707	-30.6505815749
15	4.68241827319	2.58661513435	1.02658647129	9.03739081077	-6.2816467514	6.38235641454	0.251164163983	0.650079111501	-2.16147059917	-0.853113158853	-0.17460315119	-1.34742541986	1.10736829996	0.107558159903	0.0652417541581	1.85887634421	0.453648796375	-0.36469591453	1.60135824691	-0.35218572138	1.84464443072	-35.8847249992	-58.2237256303	-33.9798290155
16	3.49042908647	1.85669165477	-2.48856598443	8.02627190341	-1.24093795219	1.7757517218	0.105867377236	0.642101497099	-2.07013874164	-1.1363155018	-0.836086933887	-0.940639911636	1.12744106361	0.73917284558	0.466881773589	2.28366895561	0.528310092258	0.109775501946	2.05306491902	-0.117324105938	2.38369466993	-30.2188487522	-64.7662990254	-29.5778183776

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 683 through 945 )	A	A	683 - 945	1 - 255
2	2	chain 'A' and (resid 946 through 1464 )	A	A	946 - 1464	256 - 765
3	3	chain 'A' and (resid 1465 through 1676 )	A	A	1465 - 1676	766 - 972
4	4	chain 'B' and (resid 20 through 130 )	B	B	20 - 130	1 - 111
5	5	chain 'B' and (resid 131 through 245 )	B	B	131 - 245	112 - 226
6	6	chain 'B' and (resid 246 through 321 )	B	B	246 - 321	227 - 302
7	7	chain 'B' and (resid 322 through 436 )	B	B	322 - 436	303 - 417
8	8	chain 'B' and (resid 437 through 490 )	B	B	437 - 490	418 - 471
9	9	chain 'B' and (resid 491 through 588 )	B	B	491 - 588	472 - 569
10	10	chain 'B' and (resid 589 through 630 )	B	B	589 - 630	570 - 603
11	11	chain 'B' and (resid 631 through 674 )	B	B	631 - 674	604 - 647
12	12	chain 'C' and (resid 1 through 5 )	C	C	1 - 5	1 - 5
13	13	chain 'C' and (resid 6 through 15 )	C	C	6 - 15	6 - 15
14	14	chain 'C' and (resid 16 through 20 )	C	C	16 - 20	16 - 20
15	15	chain 'C' and (resid 21 through 30 )	C	C	21 - 30	21 - 30
16	16	chain 'C' and (resid 31 through 35 )	C	C	31 - 35	31 - 35

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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

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-Complement C5 ... , 2 types, 2 molecules AB

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Components

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Complement C5 ... , 2 types, 2 molecules AB

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Protein/peptide / Sugars , 2 types, 2 molecules C

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Non-polymers , 2 types, 31 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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

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

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Yorodumi