[English] 日本語
Yorodumi
- PDB-3f9k: Two domain fragment of HIV-2 integrase in complex with LEDGF IBD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3f9k
TitleTwo domain fragment of HIV-2 integrase in complex with LEDGF IBD
Components
  • Integrase
  • PC4 and SFRS1-interacting protein
KeywordsVIRAL PROTEIN / RECOMBINATION / Protein-protein complex / AIDS / DNA integration / endonuclease / magnesium / metal-binding / multifunctional enzyme / nuclease / nucleotidyltransferase / nucleus / transferase / viral nucleoprotein / virion / DNA-binding / host-virus interaction / transcription / transcription regulation / zinc binding / HHCC motif
Function / homology
Function and homology information


HIV-2 retropepsin / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Formation of WDR5-containing histone-modifying complexes / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition ...HIV-2 retropepsin / supercoiled DNA binding / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Formation of WDR5-containing histone-modifying complexes / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / mRNA 5'-splice site recognition / heterochromatin / nuclear periphery / euchromatin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / response to heat / viral nucleocapsid / DNA-binding transcription factor binding / DNA recombination / response to oxidative stress / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / transcription coactivator activity / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / chromatin remodeling / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / chromatin binding / structural molecule activity / host cell plasma membrane / virion membrane / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Integrase, N-terminal zinc-binding domain / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / Transcription Elongation Factor S-II; Chain A / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. ...Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 / Integrase, N-terminal zinc-binding domain / Lens epithelium-derived growth factor, integrase-binding domain / HIV integrase-binding domain superfamily / Lens epithelium-derived growth factor (LEDGF) / Transcription Elongation Factor S-II; Chain A / TFIIS/LEDGF domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / gag protein p24 N-terminal domain / Ribonuclease H-like superfamily/Ribonuclease H / 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 / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PC4 and SFRS1-interacting protein / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHare, S. / Cherepanov, P.
CitationJournal: Plos Pathog. / Year: 2009
Title: A novel co-crystal structure affords the design of gain-of-function lentiviral integrase mutants in the presence of modified PSIP1/LEDGF/p75
Authors: Hare, S. / Shun, M.C. / Gupta, S.S. / Valkov, E. / Engelman, A. / Cherepanov, P.
History
DepositionNov 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrase
B: Integrase
C: PC4 and SFRS1-interacting protein
E: Integrase
F: Integrase
G: PC4 and SFRS1-interacting protein
I: Integrase
J: Integrase
K: PC4 and SFRS1-interacting protein
M: Integrase
N: Integrase
O: PC4 and SFRS1-interacting protein
Q: Integrase
R: Integrase
S: PC4 and SFRS1-interacting protein
U: Integrase
V: Integrase
W: PC4 and SFRS1-interacting protein
Y: Integrase
Z: Integrase
a: PC4 and SFRS1-interacting protein
c: Integrase
d: Integrase
e: PC4 and SFRS1-interacting protein
g: Integrase
h: Integrase
i: PC4 and SFRS1-interacting protein
k: Integrase
l: Integrase
m: PC4 and SFRS1-interacting protein
o: Integrase
p: Integrase
q: PC4 and SFRS1-interacting protein
s: Integrase
t: Integrase
u: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)703,19484
Polymers701,04036
Non-polymers2,15348
Water0
1
A: Integrase
B: Integrase
C: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5997
Polymers58,4203
Non-polymers1794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: Integrase
F: Integrase
G: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5997
Polymers58,4203
Non-polymers1794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
I: Integrase
J: Integrase
K: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5997
Polymers58,4203
Non-polymers1794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
M: Integrase
N: Integrase
O: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5997
Polymers58,4203
Non-polymers1794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
Q: Integrase
R: Integrase
S: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5997
Polymers58,4203
Non-polymers1794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
U: Integrase
V: Integrase
W: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5997
Polymers58,4203
Non-polymers1794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
Y: Integrase
Z: Integrase
a: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5997
Polymers58,4203
Non-polymers1794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
c: Integrase
d: Integrase
e: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5997
Polymers58,4203
Non-polymers1794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
9
g: Integrase
h: Integrase
i: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5997
Polymers58,4203
Non-polymers1794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
10
k: Integrase
l: Integrase
m: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5997
Polymers58,4203
Non-polymers1794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
11
o: Integrase
p: Integrase
q: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5997
Polymers58,4203
Non-polymers1794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
12
s: Integrase
t: Integrase
u: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5997
Polymers58,4203
Non-polymers1794
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
13
E: Integrase
F: Integrase
G: PC4 and SFRS1-interacting protein
U: Integrase
V: Integrase
W: PC4 and SFRS1-interacting protein
g: Integrase
h: Integrase
i: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,79821
Polymers175,2609
Non-polymers53812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21630 Å2
ΔGint-152 kcal/mol
Surface area57310 Å2
MethodPISA
14
A: Integrase
B: Integrase
C: PC4 and SFRS1-interacting protein
I: Integrase
J: Integrase
K: PC4 and SFRS1-interacting protein
Y: Integrase
Z: Integrase
a: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,79821
Polymers175,2609
Non-polymers53812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21720 Å2
ΔGint-151 kcal/mol
Surface area57190 Å2
MethodPISA
15
k: Integrase
l: Integrase
m: PC4 and SFRS1-interacting protein
o: Integrase
p: Integrase
q: PC4 and SFRS1-interacting protein
s: Integrase
t: Integrase
u: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,79821
Polymers175,2609
Non-polymers53812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21600 Å2
ΔGint-150 kcal/mol
Surface area57380 Å2
MethodPISA
16
M: Integrase
N: Integrase
O: PC4 and SFRS1-interacting protein
Q: Integrase
R: Integrase
S: PC4 and SFRS1-interacting protein
c: Integrase
d: Integrase
e: PC4 and SFRS1-interacting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,79821
Polymers175,2609
Non-polymers53812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21690 Å2
ΔGint-151 kcal/mol
Surface area57250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.360, 202.500, 280.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
31I
41M
51Q
61U
71Y
81c
91g
101k
111o
121s
12B
22F
32J
42N
52R
62V
72Z
82d
92h
102l
112p
122t
13C
23G
33K
43O
53S
63W
73a
83e
93i
103m
113q
123u

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A4 - 207
2112E - A4 - 207
3112I - A4 - 207
4112M - A4 - 207
5112Q - A4 - 207
6112U - A4 - 207
7112Y - A4 - 207
8112c - A4 - 207
9112g - A4 - 207
10112k - A4 - 207
11112o - A4 - 207
12112s - A4 - 207
1122B - A1 - 206
2122F - A1 - 206
3122J - A1 - 206
4122N - A1 - 206
5122R - A1 - 206
6122V - A1 - 206
7122Z - A1 - 206
8122d - A1 - 206
9122h - A1 - 206
10122l - A1 - 206
11122p - A1 - 206
12122t - A1 - 206
1132C - A347 - 379
2132G - A347 - 379
3132K - A347 - 379
4132O - A347 - 379
5132S - A347 - 379
6132W - A347 - 379
7132a - A347 - 379
8132e - A347 - 379
9132i - A347 - 379
10132m - A347 - 379
11132q - A347 - 379
12132u - A347 - 379
1232C - A395 - 419
2232G - A395 - 419
3232K - A395 - 419
4232O - A395 - 419
5232S - A395 - 419
6232W - A395 - 419
7232a - A395 - 419
8232e - A395 - 419
9232i - A395 - 419
10232m - A395 - 419
11232q - A395 - 419
12232u - A395 - 419

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein ...
Integrase /


Mass: 23672.033 Da / Num. of mol.: 24
Fragment: N-terminal and catalytic domains, UNP residues 1173-1380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 2 / Gene: gag-pol / Plasmid: pCDF-HIV2-IN(NTD+CCD) / Production host: Escherichia coli (E. coli) / Strain (production host): PC2 / References: UniProt: P04584
#2: Protein
PC4 and SFRS1-interacting protein / LEDGF / Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52 / Dense fine ...LEDGF / Lens epithelium-derived growth factor / Transcriptional coactivator p75/p52 / Dense fine speckles 70 kDa protein / DFS 70 / CLL-associated antigen KW-7


Mass: 11075.970 Da / Num. of mol.: 12
Fragment: LEDGF, Integrase binding domain, UNP residues 347-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSIP1, DFS70, LEDGF, PSIP2 / Plasmid: pES-IBD-3C7 / Production host: Escherichia coli (E. coli) / Strain (production host): PC2 / References: UniProt: O75475
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.08 Å3/Da / Density % sol: 69.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.6M sodium acetate, 10mM MgCl2, 0.1M Bis-Tris Propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9802 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9802 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 188554 / Num. obs: 188411 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Rmerge(I) obs: 0.161 / Rsym value: 0.161 / Net I/σ(I): 13
Reflection shellResolution: 3.2→3.37 Å / % possible obs: 100 % / Redundancy: 8 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.562 / % possible all: 100

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.4.0067refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B4J (chains A and C), 1K6Y (chain A residue 1-43)

2b4j

1k6y


Resolution: 3.2→34.99 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.879 / Redundancy reflection obs: 7.9 / SU B: 17.513 / SU ML: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.374 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, The structure was refined also with PHENIX
RfactorNum. reflection% reflectionSelection details
Rfree0.23421 9726 5.2 %THIN SHELLS
Rwork0.22489 ---
obs0.22538 178727 100 %-
all-178727 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 3.2→34.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46692 0 48 0 46740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02247580
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9481.93364248
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.86755880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02924.8352184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.683158712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.85715252
X-RAY DIFFRACTIONr_chiral_restr0.0670.27356
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02135124
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1531.529424
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34247616
X-RAY DIFFRACTIONr_scbond_it2.782318156
X-RAY DIFFRACTIONr_scangle_it5.1784.516632
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A816tight positional0.010.05
12F816tight positional0.010.05
13K816tight positional0.010.05
14Q816tight positional0.010.05
15V816tight positional0.010.05
16a816tight positional0.010.05
17g816tight positional0.010.05
18c816tight positional0.010.05
19g816tight positional0.010.05
110k816tight positional0.010.05
111o816tight positional0.010.05
112s816tight positional0.010.05
21B784tight positional0.010.05
22G784tight positional0.010.05
23M784tight positional0.010.05
24R784tight positional0.010.05
25W784tight positional0.010.05
26c784tight positional0.010.05
27h784tight positional0.010.05
28d784tight positional0.010.05
29h784tight positional0.010.05
210l784tight positional0.010.05
211p784tight positional0.010.05
212t784tight positional0.010.05
31C232tight positional0.010.05
32I232tight positional0.010.05
33N232tight positional0.010.05
34S232tight positional0.010.05
35Y232tight positional0.010.05
36d232tight positional0.010.05
37a232tight positional0.010.05
38e232tight positional0.010.05
39i232tight positional0.010.05
310m232tight positional0.010.05
311q232tight positional0.010.05
312u232tight positional0.010.05
11A772medium positional0.010.5
12F772medium positional0.010.5
13K772medium positional0.010.5
14Q772medium positional0.010.5
15V772medium positional0.010.5
16a772medium positional0.010.5
17g772medium positional0.010.5
18c772medium positional0.020.5
19g772medium positional0.020.5
110k772medium positional0.010.5
111o772medium positional0.010.5
112s772medium positional0.010.5
21B758medium positional0.010.5
22G758medium positional0.010.5
23M758medium positional0.010.5
24R758medium positional0.020.5
25W758medium positional0.010.5
26c758medium positional0.060.5
27h758medium positional0.010.5
28d758medium positional0.010.5
29h758medium positional0.010.5
210l758medium positional0.010.5
211p758medium positional0.010.5
212t758medium positional0.010.5
31C238medium positional0.020.5
32I238medium positional0.020.5
33N238medium positional0.010.5
34S238medium positional0.010.5
35Y238medium positional0.020.5
36d238medium positional0.020.5
37a238medium positional0.010.5
38e238medium positional0.020.5
39i238medium positional0.010.5
310m238medium positional0.010.5
311q238medium positional0.010.5
312u238medium positional0.010.5
11A816tight thermal0.020.5
12F816tight thermal0.020.5
13K816tight thermal0.010.5
14Q816tight thermal0.010.5
15V816tight thermal0.020.5
16a816tight thermal0.010.5
17g816tight thermal0.010.5
18c816tight thermal0.010.5
19g816tight thermal0.010.5
110k816tight thermal0.020.5
111o816tight thermal0.020.5
112s816tight thermal0.020.5
21B784tight thermal0.020.5
22G784tight thermal0.010.5
23M784tight thermal0.010.5
24R784tight thermal0.020.5
25W784tight thermal0.020.5
26c784tight thermal0.010.5
27h784tight thermal0.020.5
28d784tight thermal0.010.5
29h784tight thermal0.010.5
210l784tight thermal0.010.5
211p784tight thermal0.020.5
212t784tight thermal0.020.5
31C232tight thermal0.040.5
32I232tight thermal0.040.5
33N232tight thermal0.020.5
34S232tight thermal0.020.5
35Y232tight thermal0.040.5
36d232tight thermal0.040.5
37a232tight thermal0.030.5
38e232tight thermal0.040.5
39i232tight thermal0.040.5
310m232tight thermal0.040.5
311q232tight thermal0.030.5
312u232tight thermal0.030.5
11A772medium thermal0.022
12F772medium thermal0.022
13K772medium thermal0.022
14Q772medium thermal0.012
15V772medium thermal0.022
16a772medium thermal0.022
17g772medium thermal0.022
18c772medium thermal0.012
19g772medium thermal0.022
110k772medium thermal0.022
111o772medium thermal0.022
112s772medium thermal0.022
21B758medium thermal0.022
22G758medium thermal0.022
23M758medium thermal0.022
24R758medium thermal0.022
25W758medium thermal0.022
26c758medium thermal0.012
27h758medium thermal0.022
28d758medium thermal0.022
29h758medium thermal0.022
210l758medium thermal0.022
211p758medium thermal0.022
212t758medium thermal0.022
31C238medium thermal0.022
32I238medium thermal0.022
33N238medium thermal0.022
34S238medium thermal0.012
35Y238medium thermal0.022
36d238medium thermal0.022
37a238medium thermal0.022
38e238medium thermal0.022
39i238medium thermal0.022
310m238medium thermal0.022
311q238medium thermal0.022
312u238medium thermal0.022
LS refinement shellResolution: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.315 13681 -
obs-13681 100 %

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more