PDB-8dxb: HIV-1 reverse transcriptase/rilpivirine with bound fragment 5-flu...

ID or keywords:

Entry

Database: PDB / ID: 8dxb

Title

HIV-1 reverse transcriptase/rilpivirine with bound fragment 5-fluoroindole-2-carboxylic acid at the NNRTI Adjacent site

Components

Reverse transcriptase/ribonuclease H
p51 RT

Keywords

TRANSFERASE / HIV-1 reverse transcriptase

Function / homology

Function and homology information

HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...
Similarity search - Function

Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...
Similarity search - Domain/homology

Biological species

Human immunodeficiency virus type 1 group M subtype B

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Chopra, A. / Ruiz, F.X. / Bauman, J.D. / Arnold, E.

Funding support

United States, 1items

Citation

Journal: J.Med.Chem. / Year: 2023
Title: Halo Library, a Tool for Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening.
Authors: Chopra, A. / Bauman, J.D. / Ruiz, F.X. / Arnold, E.

History

Deposition	Aug 2, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 31, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8dxb.cif.gz	474.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8dxb.ent.gz	345 KB	Display	PDB format
PDBx/mmJSON format	8dxb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8dxb_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	8dxb_full_validation.pdf.gz	1.3 MB	Display
Data in XML	8dxb_validation.xml.gz	38.5 KB	Display
Data in CIF	8dxb_validation.cif.gz	52.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dx/8dxb ftp://data.pdbj.org/pub/pdb/validation_reports/dx/8dxb	HTTPS FTP

-
Related structure data

Related structure data	8dx2C 8dx3C 8dx8C 8dxeC 8dxgC 8dxhC 8dxiC 8dxjC 8dxkC 8dxlC 8dxmC 4g1qS 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	#33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #227 - Nov 2018 Telomerase similarity (1) #163 - Jul 2013 HIV Capsid similarity (1)

Deposited unit

A: Reverse transcriptase/ribonuclease H

B: p51 RT

hetero molecules

116 kDa, 2 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)	162.618, 73.128, 109.240
Angle α, β, γ (deg.)	90.000, 100.623, 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

-
Protein , 2 types, 2 molecules AB

#1: Protein	Reverse transcriptase/ribonuclease H / Exoribonuclease H / p66 RT Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: K174A, K175A, C282S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10) Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H
#2: Protein	p51 RT Mass: 50039.488 Da / Num. of mol.: 1 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate BH10) Strain: isolate BH10 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03366

#1: Protein

Reverse transcriptase/ribonuclease H / Exoribonuclease H / p66 RT

Mass: 63989.238 Da / Num. of mol.: 1 / Mutation: K174A, K175A, C282S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Production host:

Escherichia coli (E. coli)
References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H, exoribonuclease H

#2: Protein

p51 RT

Mass: 50039.488 Da / Num. of mol.: 1 / Mutation: C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Human immunodeficiency virus type 1 group M subtype B (isolate BH10)
Strain: isolate BH10 / Gene: gag-pol / Production host:

Escherichia coli (E. coli) / References: UniProt: P03366

-
Non-polymers , 6 types, 207 molecules

#3: Chemical	ChemComp-FIC / 5-fluoroindole-2-carboxylic acid Mass: 179.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₆FNO₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-T27 / 4-{[4-({4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl}amino)pyrimidin-2-yl]amino}benzonitrile / Rilpivirine Mass: 366.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₂H₁₈N₆ / Comment: medication, inhibitor*YM
#5: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56.06 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFREL NKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIF ...Details: PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFREL NKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIF QSSMTKILEPFKKQNPDIVIYQYMDDLYVGSDLEIGQHRTKIEELRQHLLRWGLTTPDKKHQKEPPFLWMGYELHPDKWT VQPIVLPEKDSWTVNDIQKLVGKLNWASQIYPGIKVRQLSKLLRGTKALTEVIPLTEEAELELAENREILKEPVHGVYYD PSKDLIAEIQKQGQGQWTYQIYQEPFKNLKTGKYARMRGAHTNDVKQLTEAVQKITTESIVIWGKTPKFKLPIQKETWET WWTEYWQATWIPEWEFVNTPPLVKLWYQ PH range: 6.4-6.6

Crystal

Density Matthews: 2.8 Å³/Da / Density % sol: 56.06 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKIGPENPYNTPVFAIKKKDSTKWRKLVDFREL NKRTQDFWEVQLGIPHPAGLKKKKSVTVLDVGDAYFSVPLDEDFRKYTAFTIPSINNETPGIRYQYNVLPQGWKGSPAIF ...
PH range: 6.4-6.6

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2019

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 72883 / % possible obs: 98.5 % / Redundancy: 3.8 % / R_merge(I) obs: 0.049 / R_pim(I) all: 0.029 / R_rim(I) all: 0.057 / Χ²: 1.063 / Net I/σ(I): 9.3 / Num. measured all: 277784

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
2.1-2.14	3.8	0.606	3565	0.731	0.356	0.704	1.065	97.7
2.14-2.18	3.9	0.506	3645	0.812	0.29	0.584	1.097	97.6
2.18-2.22	3.9	0.445	3556	0.825	0.256	0.515	1.101	97.7
2.22-2.26	3.9	0.389	3599	0.866	0.225	0.45	1.184	97.8
2.26-2.31	3.8	0.337	3585	0.888	0.197	0.391	1.117	97.9
2.31-2.37	3.7	0.276	3622	0.915	0.166	0.323	1.098	98.1
2.37-2.42	3.7	0.24	3638	0.935	0.143	0.28	1.054	98.1
2.42-2.49	3.9	0.201	3595	0.961	0.115	0.232	1.015	98.3
2.49-2.56	3.7	0.163	3601	0.969	0.097	0.19	1.03	98.2
2.56-2.65	3.8	0.138	3625	0.98	0.08	0.159	0.998	98.4
2.65-2.74	3.9	0.117	3664	0.984	0.067	0.136	0.976	98.5
2.74-2.85	3.9	0.094	3618	0.99	0.054	0.109	0.987	98.4
2.85-2.98	3.8	0.077	3649	0.992	0.045	0.09	1.023	98.6
2.98-3.14	3.7	0.066	3652	0.993	0.039	0.077	1.039	99
3.14-3.33	3.8	0.055	3671	0.995	0.032	0.064	1.007	98.9
3.33-3.59	3.9	0.048	3666	0.996	0.028	0.056	1.131	99.1
3.59-3.95	3.9	0.041	3682	0.997	0.024	0.047	1.027	99.2
3.95-4.52	3.7	0.039	3716	0.997	0.023	0.046	1.019	99.3
4.52-5.7	3.8	0.035	3733	0.998	0.02	0.041	1.132	99.6
5.7-50	3.7	0.035	3801	0.998	0.02	0.041	1.166	99.3

-
Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX	dev_3051	refinement
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4G1Q

4g1q

Resolution: 2.1→36.56 Å / SU ML: 0.2989 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.6265
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2349	3821	2.73 %
R_work	0.2129	136312	-
obs	0.2135	72874	96.55 %

Solvent computation

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

Displacement parameters

B_iso mean: 70.69 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→36.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7949	0	103	191	8243

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0032	8334
X-RAY DIFFRACTION	f_angle_d	0.6194	11326
X-RAY DIFFRACTION	f_chiral_restr	0.0452	1222
X-RAY DIFFRACTION	f_plane_restr	0.0039	1454
X-RAY DIFFRACTION	f_dihedral_angle_d	18.5977	3170

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 (%)
2.1-2.12	0.3652	133	0.3337	4665	X-RAY DIFFRACTION	89.62
2.12-2.15	0.3719	138	0.3116	5046	X-RAY DIFFRACTION	96.2
2.15-2.18	0.3121	138	0.2939	5025	X-RAY DIFFRACTION	95.84
2.18-2.21	0.3098	145	0.2926	4971	X-RAY DIFFRACTION	96.04
2.21-2.24	0.301	137	0.2955	5023	X-RAY DIFFRACTION	96.05
2.24-2.28	0.3195	143	0.2833	5098	X-RAY DIFFRACTION	96.08
2.28-2.32	0.2969	143	0.2802	4943	X-RAY DIFFRACTION	96.34
2.32-2.36	0.3274	139	0.268	5118	X-RAY DIFFRACTION	96
2.36-2.4	0.2614	137	0.2697	4957	X-RAY DIFFRACTION	95.36
2.4-2.45	0.2684	137	0.2629	5009	X-RAY DIFFRACTION	96.49
2.45-2.5	0.3102	143	0.2643	5021	X-RAY DIFFRACTION	96.31
2.5-2.55	0.3043	139	0.2685	5012	X-RAY DIFFRACTION	95.12
2.55-2.61	0.3227	142	0.2705	4987	X-RAY DIFFRACTION	95.42
2.61-2.67	0.338	138	0.2676	5056	X-RAY DIFFRACTION	96.74
2.67-2.75	0.2735	141	0.2587	5074	X-RAY DIFFRACTION	97.28
2.75-2.83	0.2723	142	0.2444	5083	X-RAY DIFFRACTION	97.08
2.83-2.92	0.2732	145	0.239	5129	X-RAY DIFFRACTION	97.56
2.92-3.02	0.2848	144	0.2476	5027	X-RAY DIFFRACTION	96.65
3.02-3.14	0.2477	144	0.2546	5074	X-RAY DIFFRACTION	97.3
3.14-3.29	0.2926	147	0.2307	5148	X-RAY DIFFRACTION	97.96
3.29-3.46	0.2115	143	0.2177	5069	X-RAY DIFFRACTION	96.59
3.46-3.68	0.2081	144	0.2083	5168	X-RAY DIFFRACTION	98.68
3.68-3.96	0.2187	142	0.1894	5094	X-RAY DIFFRACTION	98.37
3.96-4.36	0.1782	147	0.1724	5132	X-RAY DIFFRACTION	97.7
4.36-4.99	0.1714	145	0.1717	5133	X-RAY DIFFRACTION	98.36
4.99-6.28	0.2797	141	0.1893	5121	X-RAY DIFFRACTION	97.73
6.28-36.56	0.1743	144	0.1713	5129	X-RAY DIFFRACTION	97.9

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	0.599063266126	-0.369869887354	0.022796460957	0.213298622854	0.508255212979	0.672702898425	0.244665273442	-0.136636766221	-0.19203406895	0.423239893246	-0.0739732849322	0.0310778362983	0.0569450266412	0.176446147267	0.00177181921593	0.725714760872	0.00481156067947	0.0924604581595	0.557444552992	0.0201747833715	0.436458555323	46.465585716	-15.7284403692	70.2917751231
2	-0.0541181599229	0.366731184149	0.423237570793	0.062279472688	0.0661562756804	0.4750855406	0.307746591988	0.00147090240186	-0.0418031719146	0.197227953154	0.0616713167387	-0.0984562436891	0.180642658571	-0.35462760192	0.0380415695813	0.639970143258	-0.00184311548775	-0.0214057233161	0.447672738691	0.0644853857141	0.412079426319	41.4287991412	-19.5700918108	54.4337466477
3	0.185079127312	-0.211917906922	0.156380232901	0.0694480929045	0.169033080735	0.240406426937	0.121755848394	-0.350657601992	-0.00235204878708	0.304880943725	0.194467567481	0.129953081994	0.299959850323	0.112444959285	0.0067861472662	0.711219332811	-0.0532406873421	0.0677567766836	0.548079709136	0.0477698870602	0.373894902424	47.8695854631	-17.464357867	66.5428922086
4	0.497480840275	-0.100891428977	0.223520987763	0.50322769763	0.0121690736978	0.896612149333	0.337313933315	-0.193737229794	-0.458230619852	0.418585369954	0.0982195128613	-0.126361882486	0.441535437127	-0.070721371239	0.0443059630475	0.612554135471	-0.0392493116384	-0.116104442876	0.473089993104	0.0373696619505	0.536453028705	51.1564357631	-28.6308010165	42.9609917049
5	0.041591403635	-0.046314641349	0.227223899164	0.548674701163	-0.208304902605	1.44070077716	0.163135546685	-0.0921835564127	-0.173484505644	0.161190336803	0.130123214189	0.33908188897	0.0972603664009	-0.327627915778	1.79042607636E-8	0.356354184984	0.00234915113522	0.00271913688046	0.391880707357	0.0680739779509	0.537937499785	29.6427598341	-19.5657793418	24.7094073174
6	1.23050075078	-0.748372859706	0.940789920045	-0.0225397462989	-0.233196113834	0.79990594074	0.0198490557194	-0.0862137711647	-0.200518589073	0.0412687911181	0.0994128147056	0.129711892282	0.123488146156	-0.181497134146	0.00263140275989	0.238464455787	-0.0102015885797	0.0396202643491	0.368667806345	0.0148018019599	0.430799250771	20.8813074918	2.46009463144	6.57340201765
7	0.775951931514	0.565504929647	0.431153796838	0.653131005356	0.636908745394	1.57140081375	-0.159959166105	-0.540262721487	-0.258308272571	0.108622381752	0.118409449785	0.168902495326	-0.22801885881	-0.100627049207	-0.0037213189717	0.289463907948	0.0703226731305	0.037312155427	0.500983606842	0.0806192012903	0.548362231441	15.3450856752	8.85116106387	7.52840384234
8	0.834400236983	-0.436305217206	0.681090072971	1.26051928311	-0.604812232218	0.862928722678	-0.0968744542318	-0.0944566120972	-0.0335750668863	0.276628531132	-0.0845640322297	0.108608881908	-0.178254041187	0.260348515254	-0.00118048127419	0.466711097353	-0.0484497462084	-0.0013958953538	0.44746413139	-0.00827569517418	0.343697782735	56.3642223569	1.30331108768	36.6827658705
9	-0.0312224155553	-0.0644845321996	-0.0269443005173	0.152305380149	-0.0203031105596	0.0686962295982	-0.191809486503	0.161550922772	0.793933987524	0.156653101573	0.0411149647705	0.103783793259	-0.299015341026	0.116483299543	-0.115934430432	0.889591589024	-0.193031003889	-0.0692328572396	0.458941620123	0.137892219428	0.953101307999	55.6197014718	26.0309960888	33.6859239326
10	1.14825001783	-0.739546158333	0.91213981247	1.82358651279	0.33444830759	0.746562216155	-0.215589737281	0.0630700063385	0.308008353088	0.860475721231	0.100479566882	-0.149041561117	-0.152996510767	0.464034937007	-0.0862103559338	0.556133567782	-0.204012923749	-0.158687601932	0.415149335643	0.0166129070216	0.364139837091	61.8629431681	9.01376932395	37.4905284398
11	0.263599565066	0.0815583277229	0.230151663969	0.210029199903	0.313671008456	0.394033006537	0.0954788290582	0.732130773504	-0.00894475137203	0.414741033504	0.351937482445	-0.675503846484	0.769322364427	0.717785286223	1.11944358762	0.332420169095	-0.722519141584	0.0604460581823	0.805829866175	0.607275774982	0.727843939432	67.8403205267	19.324268955	22.1235565444
12	0.84981315251	0.0722166221705	0.373032923785	1.79847057677	-0.438109413168	1.50914755644	-0.180816726156	0.0941904728652	0.278289539603	0.25814793497	-0.00529183881708	-0.0300045741771	-0.277942650359	0.0599444991635	-6.72882923925E-6	0.346126565156	-0.0506815933809	0.0218003432154	0.355012972868	-0.0246075726853	0.346701594988	32.7357493393	24.9382487141	7.76611115569
13	0.767248254212	0.0604327169584	0.411900092267	0.913277186134	0.0122594537924	0.711098656386	-0.0688089600329	0.102115091862	0.0962877184604	0.17579057118	-0.132965312804	0.10034373536	-0.162185950614	0.0326386625343	4.62961266899E-8	0.4219758497	-0.0531633991184	0.00780651661428	0.323485612527	-0.00175200942975	0.356107410823	43.1116879142	10.3761704566	19.9732533478

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 -1 through 59 )	A	A	-1 - 59	1 - 61
2	2	chain 'A' and (resid 60 through 104 )	A	A	60 - 104	62 - 106
3	3	chain 'A' and (resid 105 through 155 )	A	A	105 - 155	107 - 157
4	4	chain 'A' and (resid 156 through 253 )	A	A	156 - 253	158 - 255
5	5	chain 'A' and (resid 254 through 383 )	A	A	254 - 383	256 - 385
6	6	chain 'A' and (resid 384 through 499 )	A	A	384 - 499	386 - 501
7	7	chain 'A' and (resid 500 through 554 )	A	A	500 - 554	502 - 556
8	8	chain 'B' and (resid 5 through 83 )	B	D	5 - 83	1 - 79
9	9	chain 'B' and (resid 84 through 104 )	B	D	84 - 104	80 - 100
10	10	chain 'B' and (resid 105 through 174 )	B	D	105 - 174	101 - 170
11	11	chain 'B' and (resid 175 through 238 )	B	D	175 - 238	171 - 225
12	12	chain 'B' and (resid 239 through 363 )	B	D	239 - 363	226 - 350
13	13	chain 'B' and (resid 364 through 428 )	B	D	364 - 428	351 - 415

-
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 , 2 types, 2 molecules AB

-
Non-polymers , 6 types, 207 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 , 2 types, 2 molecules AB

-Non-polymers , 6 types, 207 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 , 2 types, 2 molecules AB

-
Non-polymers , 6 types, 207 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