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- PDB-3n96: Crystal structure of human CRFR2 alpha extracellular domain in co... -

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Basic information

Entry
Database: PDB / ID: 3n96
TitleCrystal structure of human CRFR2 alpha extracellular domain in complex with Urocortin 1
Components
  • Maltose binding protein-CRFR2 alpha
  • Urocortin
KeywordsMembrane protein / Hormone / Class B-GPCR / Extracellular domain / CRFR2 alpha extracellular domain / Neuropeptide / Selectivity
Function / homology
Function and homology information


histone deacetylase inhibitor activity / corticotropin-releasing hormone receptor 2 binding / positive regulation of corticotropin secretion / positive regulation of behavioral fear response / varicosity / negative regulation of hormone secretion / drinking behavior / response to auditory stimulus / negative regulation of appetite / corticotropin-releasing hormone receptor 1 binding ...histone deacetylase inhibitor activity / corticotropin-releasing hormone receptor 2 binding / positive regulation of corticotropin secretion / positive regulation of behavioral fear response / varicosity / negative regulation of hormone secretion / drinking behavior / response to auditory stimulus / negative regulation of appetite / corticotropin-releasing hormone receptor 1 binding / neuropeptide hormone activity / positive regulation of vascular permeability / negative regulation of cell size / Class B/2 (Secretin family receptors) / response to pain / negative regulation of feeding behavior / detection of maltose stimulus / positive regulation of calcium ion import / maltose transport complex / startle response / carbohydrate transport / positive regulation of cAMP/PKA signal transduction / positive regulation of collagen biosynthetic process / associative learning / social behavior / Synthesis, secretion, and deacylation of Ghrelin / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / neuropeptide signaling pathway / maltodextrin transmembrane transport / regulation of synaptic transmission, glutamatergic / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of blood pressure / axon terminus / positive regulation of cardiac muscle contraction / ATP-binding cassette (ABC) transporter complex / response to glucocorticoid / aerobic respiration / positive regulation of translation / positive regulation of DNA replication / cell chemotaxis / sensory perception of sound / female pregnancy / positive regulation of interleukin-6 production / vasodilation / neuron projection development / response to estradiol / outer membrane-bounded periplasmic space / positive regulation of cell growth / response to oxidative stress / perikaryon / negative regulation of neuron apoptotic process / periplasmic space / G protein-coupled receptor signaling pathway / negative regulation of gene expression / dendrite / DNA damage response / positive regulation of transcription by RNA polymerase II / extracellular region / membrane
Similarity search - Function
Urocortin/corticotropin-releasing factor / Corticotropin-releasing factor conserved site / Corticotropin-releasing factor family signature. / corticotropin-releasing factor / Corticotropin-releasing factor / Corticotropin-releasing factor family / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / Hormone receptor domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...Urocortin/corticotropin-releasing factor / Corticotropin-releasing factor conserved site / Corticotropin-releasing factor family signature. / corticotropin-releasing factor / Corticotropin-releasing factor / Corticotropin-releasing factor family / GPCR, family 2, extracellular hormone receptor domain / Hormone receptor fold / Hormone receptor domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Urocortin
Similarity search - Component
Biological speciesHomo sapiens (human)
Homo Sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPal, K. / Swaminathan, K. / Pioszak, A.A. / Xu, H.E.
CitationJournal: To be Published
Title: Structural basis of ligand selectivity in human CRFR1 and CRFR2 alpha extracellular domain
Authors: Pal, K. / Swaminathan, K. / Pioszak, A.A. / Xu, H.E.
History
DepositionMay 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose binding protein-CRFR2 alpha
B: Maltose binding protein-CRFR2 alpha
C: Maltose binding protein-CRFR2 alpha
D: Maltose binding protein-CRFR2 alpha
E: Urocortin
F: Urocortin
G: Urocortin
H: Urocortin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,75312
Polymers220,3848
Non-polymers1,3694
Water1,856103
1
A: Maltose binding protein-CRFR2 alpha
D: Maltose binding protein-CRFR2 alpha
F: Urocortin
G: Urocortin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8766
Polymers110,1924
Non-polymers6852
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-23 kcal/mol
Surface area42820 Å2
MethodPISA
2
B: Maltose binding protein-CRFR2 alpha
C: Maltose binding protein-CRFR2 alpha
E: Urocortin
H: Urocortin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8766
Polymers110,1924
Non-polymers6852
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-25 kcal/mol
Surface area42530 Å2
MethodPISA
3
A: Maltose binding protein-CRFR2 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4892
Polymers53,1471
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Maltose binding protein-CRFR2 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4892
Polymers53,1471
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: Maltose binding protein-CRFR2 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4892
Polymers53,1471
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
D: Maltose binding protein-CRFR2 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4892
Polymers53,1471
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
E: Urocortin


  • defined by author
  • 1.95 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,9491
Polymers1,9491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
F: Urocortin


  • defined by author
  • 1.95 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)1,9491
Polymers1,9491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
G: Urocortin


Theoretical massNumber of molelcules
Total (without water)1,9491
Polymers1,9491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
H: Urocortin


Theoretical massNumber of molelcules
Total (without water)1,9491
Polymers1,9491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.063, 211.551, 107.839
Angle α, β, γ (deg.)90.000, 104.370, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12B
22C
13C
23D
14A
24B
15B
25C
16C
26D
17B
27C
18C
28D
19E
29F
110F
210G
111G
211H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSALAALA1AA-369 - -63 - 366
21LYSLYSALAALA1BB-369 - -63 - 366
12LYSLYSALAALA1BB-369 - -63 - 366
22LYSLYSALAALA1CC-369 - -63 - 366
13LYSLYSALAALA1CC-369 - -63 - 366
23LYSLYSALAALA1DD-369 - -63 - 366
14ALAALAILEILE2AA4 - 101376 - 473
24ALAALAILEILE2BB4 - 101376 - 473
15ALAALAPROPRO2BB4 - 30376 - 402
25ALAALAPROPRO2CC4 - 30376 - 402
16ALAALAPROPRO2CC4 - 30376 - 402
26ALAALAPROPRO2DD4 - 30376 - 402
17PROPROILEILE2BB36 - 101408 - 473
27PROPROILEILE2CC36 - 101408 - 473
18PROPROILEILE2CC36 - 101408 - 473
28PROPROILEILE2DD36 - 101408 - 473
19ALAALAVALVAL2EE31 - 416 - 16
29ALAALAVALVAL2FF31 - 416 - 16
110ALAALAVALVAL2FF31 - 416 - 16
210ALAALAVALVAL2GG31 - 416 - 16
111GLNGLNVALVAL2GG33 - 418 - 16
211GLNGLNVALVAL2HH33 - 418 - 16

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11

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Components

#1: Protein
Maltose binding protein-CRFR2 alpha


Mass: 53146.746 Da / Num. of mol.: 4 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRFR2 alpha / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9*PLUS
#2: Protein/peptide
Urocortin


Mass: 1949.134 Da / Num. of mol.: 4 / Fragment: UNP residues 107-122 / Source method: obtained synthetically / Source: (synth.) Homo Sapiens (human) / References: UniProt: P55089
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 10% PEG 6000 0.1M Sodium acetate(pH 4.6) 0.1M MgCl2 14% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1.07818 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07818 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 59140 / % possible obs: 95.52 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.141 / Net I/σ(I): 12.6
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N93

3n93


Resolution: 2.75→50 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 1 / SU B: 34.316 / SU ML: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2922 5 %RANDOM
Rwork0.235 ---
obs0.237 58007 95.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 157.23 Å2 / Biso mean: 62.237 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å2-3.9 Å2
2--0.38 Å20 Å2
3----0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15054 0 92 103 15249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02215530
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.96821122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38551925
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45625.581697
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.725152528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5951546
X-RAY DIFFRACTIONr_chiral_restr0.10.22306
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02111846
X-RAY DIFFRACTIONr_mcbond_it0.2091.59641
X-RAY DIFFRACTIONr_mcangle_it0.323215441
X-RAY DIFFRACTIONr_scbond_it0.51635885
X-RAY DIFFRACTIONr_scangle_it0.7934.55681
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2826TIGHT POSITIONAL0.040.05
1A2826TIGHT THERMAL0.110.5
2B2826TIGHT POSITIONAL0.080.05
2B2826TIGHT THERMAL0.120.5
3C2826TIGHT POSITIONAL0.040.05
3C2826TIGHT THERMAL0.080.5
4A392TIGHT POSITIONAL0.050.05
4A369MEDIUM POSITIONAL0.060.5
4A392TIGHT THERMAL0.080.5
4A369MEDIUM THERMAL0.12
5B108TIGHT POSITIONAL0.10.05
5B91MEDIUM POSITIONAL0.140.5
5B108TIGHT THERMAL0.130.5
5B91MEDIUM THERMAL0.152
6C108TIGHT POSITIONAL0.050.05
6C91MEDIUM POSITIONAL0.080.5
6C108TIGHT THERMAL0.090.5
6C91MEDIUM THERMAL0.132
7B264TIGHT POSITIONAL0.080.05
7B262MEDIUM POSITIONAL0.120.5
7B264TIGHT THERMAL0.10.5
7B262MEDIUM THERMAL0.132
8C264TIGHT POSITIONAL0.040.05
8C262MEDIUM POSITIONAL0.060.5
8C264TIGHT THERMAL0.10.5
8C262MEDIUM THERMAL0.132
9E44TIGHT POSITIONAL0.030.05
9E46MEDIUM POSITIONAL0.040.5
9E44TIGHT THERMAL0.060.5
9E46MEDIUM THERMAL0.062
10F44TIGHT POSITIONAL0.040.05
10F46MEDIUM POSITIONAL0.070.5
10F44TIGHT THERMAL0.070.5
10F46MEDIUM THERMAL0.082
11G36TIGHT POSITIONAL0.030.05
11G40MEDIUM POSITIONAL0.040.5
11G36TIGHT THERMAL0.030.5
11G40MEDIUM THERMAL0.032
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 213 -
Rwork0.305 4161 -
all-4374 -
obs--98.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.0239-0.0677-0.53271.6021.01333.010.1199-0.06950.0582-0.0167-0.0601-0.1138-0.0862-0.0501-0.05980.0142-0.00770.00790.0129-0.00980.03192.998232.098731.0533
21.07950.09620.53161.72711.02342.88960.12750.0495-0.04580.0478-0.0323-0.06040.0916-0.031-0.09530.0306-0.00290.01490.0084-0.01150.0363-23.938971.739773.4496
31.44420.5265-0.39722.47420.50522.58690.0353-0.2831-0.21770.4215-0.0370.15490.5036-0.05780.00180.1990.00080.05140.12790.02960.1231-27.799475.833515.209
41.4398-0.44790.38242.37320.63392.76460.01390.2690.2073-0.5059-0.01990.1453-0.5122-0.05710.0060.2032-0.00680.00980.12730.01890.1068-0.461228.038289.2535
55.86452.1063-1.0693.7047-1.08680.68140.0179-0.14350.11210.056-0.0203-0.1164-0.11580.28080.00240.0848-0.0399-0.00630.2583-0.0460.104814.46428.126754.7621
65.0704-2.17570.91493.0040.09371.51930.06470.2311-0.19890.02790.004-0.1470.12510.226-0.06870.0912-0.02040.0860.2024-0.03090.1483-12.767695.686549.1547
74.62510.8893-0.76382.6287-2.96223.4046-0.04670.00050.09260.06460.11850.1313-0.1157-0.1324-0.07180.07290.0273-0.01470.1188-0.02420.138-40.433695.179450.7971
84.5625-0.56470.80913.2163-2.39952.3416-0.065-0.0166-0.1260.0170.08390.0620.1327-0.153-0.01890.0586-0.0420.04560.1262-0.02160.09-13.43398.640754.0161
91.1389-1.18743.60911.2469-3.799411.78280.42840.028-0.121-0.26560.10820.20950.68540.5336-0.53670.84520.04190.13261.10050.05340.861917.728916.527136.4345
105.0012.5389-15.07631.29-7.658945.51390.5736-0.42530.1050.2551-0.13640.0799-1.32331.3434-0.43711.0975-0.0907-0.26940.8888-0.03670.8042-9.110486.115965.0128
119.3121-2.0621-10.495413.9048-12.698928.81340.24731.12170.1064-1.58410.0494-0.03881.2552-1.1993-0.29670.3973-0.29280.08511.0107-0.340.2756-43.565488.784432.0187
125.72846.73250.10412.5675-9.848923.44620.3817-0.6454-0.09091.4515-0.1753-0.2498-1.082-0.358-0.20640.7470.4545-0.11080.7021-0.34620.3079-16.624215.235172.4985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-369 - 2
2X-RAY DIFFRACTION2B-369 - 2
3X-RAY DIFFRACTION3C-369 - 2
4X-RAY DIFFRACTION4D-369 - 2
5X-RAY DIFFRACTION5A3 - 103
6X-RAY DIFFRACTION6B3 - 101
7X-RAY DIFFRACTION7C3 - 102
8X-RAY DIFFRACTION8D3 - 103
9X-RAY DIFFRACTION9G28 - 41
10X-RAY DIFFRACTION10H32 - 41
11X-RAY DIFFRACTION11E26 - 41
12X-RAY DIFFRACTION12F26 - 41

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  • 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

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