PDB-7n9x: CA-targeting nanobody is a tool for studying HIV-1 capsid lattice...

ID or keywords:

Entry

Database: PDB / ID: 7n9x

Title

CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions

Components

(Nanobody) x 3
Capsid protein
Peptidyl-prolyl cis-trans isomerase A

Keywords

VIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 / hexamer / nanobody / CypA / VIRAL PROTEIN-IMMUNE SYSTEM complex

Function / homology

Function and homology information

negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / negative regulation of viral life cycle / lipid droplet organization / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / endothelial cell activation / Basigin interactions / protein peptidyl-prolyl isomerization / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / viral release from host cell / negative regulation of protein phosphorylation / Calcineurin activates NFAT / Binding and entry of HIV virion / positive regulation of viral genome replication / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / neutrophil chemotaxis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / peptidyl-prolyl cis-trans isomerase activity / negative regulation of protein kinase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / positive regulation of protein secretion / peptidylprolyl isomerase / Assembly Of The HIV Virion / Budding and maturation of HIV virion / platelet activation / platelet aggregation / neuron differentiation / positive regulation of NF-kappaB transcription factor activity / SARS-CoV-1 activates/modulates innate immune responses / integrin binding / unfolded protein binding / Platelet degranulation / protein folding / positive regulation of protein phosphorylation / cellular response to oxidative stress / viral nucleocapsid / secretory granule lumen / vesicle / ficolin-1-rich granule lumen / host cell cytoplasm / positive regulation of MAPK cascade / viral translational frameshifting / focal adhesion / apoptotic process / Neutrophil degranulation / host cell nucleus / virion membrane / structural molecule activity / protein-containing complex / extracellular space / RNA binding / extracellular exosome / extracellular region / zinc ion binding / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function

Biological species

Human immunodeficiency virus 1

Lama glama (llama)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.511 Å

Authors

Gerber, E.E. / Digianantonio, K.M. / Tripler, T.N. / Smaga, S.S. / Summers, B.J. / Xiong, Y.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	P50GM082251	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	F32 GM131426 01A1	United States

Citation

Journal: To Be Published
Title: CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions
Authors: Gerber, E.E. / Digianantonio, K.M. / Tripler, T.N. / Smaga, S.S. / Summers, B.J. / Xiong, Y.

History

Deposition	Jun 18, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 22, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7n9x.cif.gz	560.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7n9x.ent.gz		Display	PDB format
PDBx/mmJSON format	7n9x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n9/7n9x ftp://data.pdbj.org/pub/pdb/validation_reports/n9/7n9x	HTTPS FTP

-
Related structure data

Related structure data	7n9uC 7n9vC 3h47S 5o2uS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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	#163 - Jul 2013 HIV Capsid similarity (21) #136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #245 - May 2020 Spliceosomes similarity (8) #33 - Sep 2002 HIV Reverse Transcriptase similarity (7) #6 - Jun 2000 HIV-1 Protease similarity (7) #44 - Aug 2003 Calmodulin similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #196 - Apr 2016 Lead Poisoning similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1) #169 - Jan 2014 HIV Envelope Glycoprotein similarity (1) #63 - Mar 2005 T-Cell Receptor similarity (1) #128 - Aug 2010 Interferons similarity (1) #94 - Oct 2007 Superoxide Dismutase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#163 - Jul 2013
HIV Capsid
similarity (21)
#136 - Apr 2011
Nanobodies
similarity (1)
#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#245 - May 2020
Spliceosomes
similarity (8)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (7)
#6 - Jun 2000
HIV-1 Protease
similarity (7)
#44 - Aug 2003
Calmodulin
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#196 - Apr 2016
Lead Poisoning
similarity (1)
#28 - Apr 2002
Anthrax Toxin
similarity (1)
#169 - Jan 2014
HIV Envelope Glycoprotein
similarity (1)
#63 - Mar 2005
T-Cell Receptor
similarity (1)
#128 - Aug 2010
Interferons
similarity (1)
#94 - Oct 2007
Superoxide Dismutase
similarity (1)

Deposited unit

BBB: Capsid protein

CCC: Capsid protein

AAA: Capsid protein

FFF: Nanobody

EEE: Nanobody

DDD: Nanobody

GGG: Peptidyl-prolyl cis-trans isomerase A

HHH: Peptidyl-prolyl cis-trans isomerase A

III: Peptidyl-prolyl cis-trans isomerase A

165 kDa, 9 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

BBB: Capsid protein

CCC: Capsid protein

AAA: Capsid protein

FFF: Nanobody

EEE: Nanobody

DDD: Nanobody

GGG: Peptidyl-prolyl cis-trans isomerase A

HHH: Peptidyl-prolyl cis-trans isomerase A

III: Peptidyl-prolyl cis-trans isomerase A

BBB: Capsid protein

CCC: Capsid protein

AAA: Capsid protein

FFF: Nanobody

EEE: Nanobody

DDD: Nanobody

GGG: Peptidyl-prolyl cis-trans isomerase A

HHH: Peptidyl-prolyl cis-trans isomerase A

III: Peptidyl-prolyl cis-trans isomerase A

defined by author
Evidence: gel filtration
329 kDa, 18 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	127.950, 137.850, 313.832
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	PRO	PRO	CYS	CYS	BBB	A	1 - 218	1 - 218
2	2	1	PRO	PRO	CYS	CYS	CCC	B	1 - 218	1 - 218
3	3	2	PRO	PRO	GLN	GLN	BBB	A	1 - 219	1 - 219
4	4	2	PRO	PRO	GLN	GLN	AAA	C	1 - 219	1 - 219
5	5	3	PRO	PRO	CYS	CYS	CCC	B	1 - 218	1 - 218
6	6	3	PRO	PRO	CYS	CYS	AAA	C	1 - 218	1 - 218
7	7	4	ASP	ASP	THR	THR	FFF	D	1 - 110	1 - 113
8	8	4	ASP	ASP	THR	THR	EEE	E	1 - 110	1 - 111
9	9	5	VAL	VAL	VAL	VAL	FFF	D	2 - 111	2 - 114
10	10	5	VAL	VAL	VAL	VAL	DDD	F	2 - 111	1 - 113
11	11	6	VAL	VAL	THR	THR	EEE	E	2 - 110	2 - 111
12	12	6	VAL	VAL	THR	THR	DDD	F	2 - 110	1 - 112
13	13	7	ASN	ASN	LEU	LEU	GGG	G	3 - 164	3 - 164
14	14	7	ASN	ASN	LEU	LEU	HHH	H	3 - 164	3 - 164
15	15	8	MET	MET	GLU	GLU	GGG	G	1 - 165	1 - 165
16	16	8	MET	MET	GLU	GLU	III	I	1 - 165	1 - 165
17	17	9	ASN	ASN	LEU	LEU	HHH	H	3 - 164	3 - 164
18	18	9	ASN	ASN	LEU	LEU	III	I	3 - 164	3 - 164

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18

#1: Protein	Capsid protein Mass: 24542.164 Da / Num. of mol.: 3 / Fragment: UNP residues 133-354 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B6DRA0
#2: Antibody	Nanobody Mass: 12373.908 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Antibody	Nanobody Mass: 12116.620 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#4: Antibody	Nanobody Mass: 12284.817 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein	Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A Mass: 18036.504 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62937, peptidylprolyl isomerase
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.23 Å³/Da / Density % sol: 70.93 %
Crystal grow	Temperature: 295 K / Method: microbatch Details: 100 mM Bis-Tris propane, pH 6.8, 15% PEG3350, 200 mM sodium

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 1.0711 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 29, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.0711 Å / Relative weight: 1

Reflection

Resolution: 3.5→50 Å / Num. obs: 33153 / % possible obs: 95.9 % / Redundancy: 3.3 % / R_merge(I) obs: 0.182 / R_pim(I) all: 0.114 / R_rim(I) all: 0.216 / Χ²: 1.006 / Net I/σ(I): 5 / Num. measured all: 109451

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
3.5-3.56	3.3	1.179	1676	0.38	0.748	1.405	1.012	98.7
3.56-3.63	3.3	1.014	1682	0.457	0.645	1.21	1.02	98.4
3.63-3.69	3.3	0.916	1687	0.404	0.582	1	1.058	98.9
3.69-3.77	3.3	0.777	1654	0.633	0.491	0.926	0.972	98
3.77-3.85	3.3	0.782	1675	0.658	0.494	0.931	0.999	97.2
3.85-3.94	3.1	0.603	1647	0.69	0.39	0.724	1.157	96.3
3.94-4.04	3.1	0.513	1639	0.778	0.327	0.613	1.005	95.2
4.04-4.15	3.1	0.409	1471	0.869	0.252	0.485	0.964	86.4
4.15-4.27	3.3	0.347	1665	0.899	0.214	0.41	0.969	97.7
4.27-4.41	3.4	0.279	1683	0.93	0.172	0.33	1.04	99.1
4.41-4.57	3.4	0.223	1710	0.955	0.137	0.263	0.996	98.6
4.57-4.75	3.4	0.191	1677	0.97	0.118	0.226	1.023	97.7
4.75-4.97	3.3	0.171	1700	0.976	0.107	0.203	0.975	97.9
4.97-5.23	3.2	0.185	1651	0.964	0.118	0.221	0.967	95.9
5.23-5.55	3.2	0.167	1506	0.968	0.103	0.198	1.002	87.2
5.55-5.98	3.5	0.16	1710	0.968	0.098	0.189	1.01	97.6
5.98-6.58	3.5	0.119	1685	0.983	0.073	0.141	1.021	97.6
6.58-7.53	3.3	0.083	1686	0.989	0.052	0.099	1.089	95.6
7.53-9.48	3.3	0.051	1614	0.995	0.031	0.06	0.899	90.4
9.48-50	3.3	0.045	1735	0.996	0.027	0.053	0.931	93.2

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
DENZO		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries 5O2U & 3H47

5o2u

3h47

Resolution: 3.511→49.581 Å / Cor.coef. F_o:F_c: 0.915 / Cor.coef. F_o:F_c free: 0.924 / SU B: 97.604 / SU ML: 0.616 / Cross valid method: FREE R-VALUE / ESU R Free: 0.593 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2699	1668	5.033 %
R_work	0.2449	31474	-
all	0.246	-	-
obs	-	33142	94.389 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 180.204 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.4 Å²	0 Å²	-0 Å²
2-	-	2.014 Å²	0 Å²
3-	-	-	-2.414 Å²

Refinement step

Cycle: LAST / Resolution: 3.511→49.581 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11458	0	0	0	11458

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	11689
X-RAY DIFFRACTION	r_ext_dist_refined_d	0.094	0.01	15267
X-RAY DIFFRACTION	r_angle_refined_deg	1.602	1.639	15797
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.008	5	1475
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.926	22.687	588
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.578	15	1984
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.919	15	70
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1526
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	8892
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	5166
X-RAY DIFFRACTION	r_nbtor_refined	0.321	0.2	8133
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.19	0.2	325
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.314	0.2	79
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.39	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	7.218	10.227	5938
X-RAY DIFFRACTION	r_mcangle_it	11.904	15.324	7401
X-RAY DIFFRACTION	r_scbond_it	7.575	10.283	5750
X-RAY DIFFRACTION	r_scangle_it	11.721	15.292	8396
X-RAY DIFFRACTION	r_lrange_it	19.575	195.144	47452
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.158	0.05	6265
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.158	0.05	6305
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.152	0.05	6307
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.194	0.05	2874
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.231	0.05	2716
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.22	0.05	2690
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.18	0.05	4376
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.196	0.05	4483
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.184	0.05	4400

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	BBB	X-RAY DIFFRACTION	Local ncs	0.15824	0.05006
1	2	CCC	X-RAY DIFFRACTION	Local ncs	0.15824	0.05006
2	3	BBB	X-RAY DIFFRACTION	Local ncs	0.15758	0.05006
2	4	AAA	X-RAY DIFFRACTION	Local ncs	0.15758	0.05006
3	5	CCC	X-RAY DIFFRACTION	Local ncs	0.15199	0.05006
3	6	AAA	X-RAY DIFFRACTION	Local ncs	0.15199	0.05006
4	7	FFF	X-RAY DIFFRACTION	Local ncs	0.19448	0.05006
4	8	EEE	X-RAY DIFFRACTION	Local ncs	0.19448	0.05006
5	9	FFF	X-RAY DIFFRACTION	Local ncs	0.23119	0.05005
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.23119	0.05005
6	11	EEE	X-RAY DIFFRACTION	Local ncs	0.22044	0.05005
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.22044	0.05005
7	13	GGG	X-RAY DIFFRACTION	Local ncs	0.17981	0.05007
7	14	HHH	X-RAY DIFFRACTION	Local ncs	0.17981	0.05007
8	15	GGG	X-RAY DIFFRACTION	Local ncs	0.19638	0.05007
8	16	III	X-RAY DIFFRACTION	Local ncs	0.19638	0.05007
9	17	HHH	X-RAY DIFFRACTION	Local ncs	0.18436	0.05007
9	18	III	X-RAY DIFFRACTION	Local ncs	0.18436	0.05007

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
3.511-3.602	0.359	90	0.355	1911	0.355	2538	0.531	0.53	78.8416	0.351
3.602-3.7	0.373	134	0.351	2301	0.352	2474	0.624	0.632	98.4236	0.347
3.7-3.807	0.356	124	0.312	2282	0.314	2449	0.704	0.715	98.2442	0.306
3.807-3.923	0.34	103	0.321	2169	0.322	2337	0.771	0.765	97.2187	0.306
3.923-4.051	0.329	103	0.279	2092	0.282	2295	0.798	0.834	95.6427	0.265
4.051-4.192	0.25	90	0.261	1841	0.261	2198	0.881	0.881	87.8526	0.239
4.192-4.349	0.276	126	0.241	1974	0.243	2137	0.877	0.891	98.2686	0.221
4.349-4.525	0.269	97	0.227	1935	0.229	2050	0.913	0.907	99.1219	0.203
4.525-4.725	0.253	95	0.216	1844	0.218	1978	0.901	0.918	98.0283	0.191
4.725-4.953	0.243	90	0.204	1779	0.206	1916	0.917	0.927	97.547	0.182
4.953-5.218	0.274	86	0.222	1669	0.225	1812	0.897	0.906	96.8543	0.193
5.218-5.531	0.342	81	0.262	1411	0.266	1705	0.828	0.881	87.5073	0.225
5.531-5.907	0.282	64	0.258	1502	0.259	1620	0.83	0.878	96.6667	0.225
5.907-6.373	0.303	78	0.248	1392	0.251	1508	0.89	0.907	97.4801	0.211
6.373-6.97	0.247	61	0.255	1300	0.255	1402	0.901	0.908	97.0756	0.233
6.97-7.773	0.256	68	0.231	1123	0.233	1265	0.921	0.922	94.1502	0.22
7.773-8.939	0.229	53	0.18	946	0.182	1143	0.947	0.957	87.4016	0.187
8.939-10.861	0.195	53	0.163	899	0.165	979	0.966	0.969	97.2421	0.178
10.861-15.004	0.209	47	0.184	691	0.185	784	0.958	0.964	94.1327	0.203
15.004-49.581	0.197	25	0.274	413	0.268	501	0.97	0.938	87.4251	0.326

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	1.4098	0.3393	0.1451	0.8341	-0.6304	1.8346	-0.0074	-0.2698	-0.0101	-0.157	-0.0435	-0.1071	0.2185	-0.0337	0.0508	0.903	0.0111	0.1545	0.9536	0.1276	0.7936	60.432	43.366	40.9131
2	5.6617	-2.1672	-1.1706	6.2437	-0.4013	5.3937	0.2974	-0.5725	-0.2704	0.224	-0.0331	0.4526	-0.2357	0.1626	-0.2642	0.5118	-0.1969	0.3364	1.0475	0.2043	0.7177	32.4843	48.1463	64.1631
3	1.841	-0.6134	0.0649	0.729	0.0388	1.8666	-0.122	-0.0986	-0.1561	0.0014	-0.0701	0.0222	0.2198	-0.2256	0.1921	0.7431	-0.0833	0.105	1.1193	-0.0193	0.8033	40.1297	59.203	40.7232
4	2.6273	-0.2054	-1.4432	6.1251	1.5714	1.4695	-0.1617	-0.0945	-0.2665	0.0143	0.1742	-0.0268	-0.1322	-0.4466	-0.0126	0.5978	0.2369	0.0699	1.2374	-0.1424	0.6289	29.8497	85.8785	63.7466
5	0.7386	-0.1799	0.2806	2.2961	0.3064	3.6956	-0.1131	-0.1154	-0.0342	-0.1018	-0.1097	-0.04	-0.2559	-0.2015	0.2228	0.6628	0.0594	0.0002	1.0938	-0.1927	0.7814	43.6382	84.8106	40.8524
6	4.6239	1.5236	2.9599	2.9046	1.3521	2.1049	-0.1291	-0.1379	-0.0106	0.0602	-0.1504	0.2852	-0.2236	0.016	0.2796	0.8365	0.0304	-0.1556	0.9034	-0.2883	0.7206	62.203	105.9532	65.3111
7	3.9545	-0.0358	-1.6229	3.9301	-1.7157	4.6786	0.471	-0.227	0.2698	-0.132	-0.2764	0.4698	-0.7578	0.7475	-0.1945	1.1008	-0.399	-0.3393	0.7812	-0.1821	0.5447	83.1609	122.4489	68.8116
8	0.3638	-1.1898	0.6918	7.9137	-2.1785	1.5775	-0.1173	-0.0421	-0.0116	0.023	0.4348	0.5758	-0.6496	-0.1686	-0.3175	0.8612	0.463	0.2873	0.9588	-0.1665	0.607	21.887	111.2147	62.6929
9	1.5557	1.1853	1.7414	0.9418	1.1018	3.8958	0.2134	-0.6812	1.0244	0.1959	-0.4498	0.98	0.002	-0.6666	0.2364	0.0837	0.0267	0.3711	1.036	-0.2812	1.9492	6.8473	54.6685	64.7761
10	0.4065	0.0682	-1.4085	0.4532	-0.3223	6.5672	-0.5694	-0.205	0.0631	0.1221	0.173	0.261	1.5978	0.8416	0.3964	1.4895	0.4144	0.2596	0.517	0.1382	0.6603	70.8979	16.9916	16.6553
11	1.0471	-0.6267	0.1381	0.7541	1.2489	7.7742	-0.0611	-0.2382	0.5632	0.224	-0.218	-0.3258	2.0937	-1.563	0.279	1.1923	-0.7679	0.1468	1.1464	-0.2017	0.3455	23.3661	36.7977	16.4156
12	0.541	1.053	-0.846	2.4411	-0.591	7.127	-0.0211	-0.0141	-0.1553	0.1261	-0.1566	-0.5305	-0.2159	-1.9763	0.1777	0.4196	0.4145	-0.1486	1.9671	-0.2302	0.3009	15.6758	89.0308	16.6355

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	1 - 145
2	X-RAY DIFFRACTION	2	ALL	AAA	146 - 219
3	X-RAY DIFFRACTION	3	ALL	BBB	1 - 145
4	X-RAY DIFFRACTION	4	ALL	BBB	146 - 219
5	X-RAY DIFFRACTION	5	ALL	CCC	1 - 145
6	X-RAY DIFFRACTION	6	ALL	CCC	146 - 219
7	X-RAY DIFFRACTION	7	ALL	FFF	1 - 112
8	X-RAY DIFFRACTION	8	ALL	EEE	1 - 111
9	X-RAY DIFFRACTION	9	ALL	DDD	2 - 112
10	X-RAY DIFFRACTION	10	ALL	GGG	1 - 165
11	X-RAY DIFFRACTION	11	ALL	HHH	3 - 165
12	X-RAY DIFFRACTION	12	ALL	III	1 - 165

-
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