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- PDB-3sku: Herpes simplex virus glycoprotein D bound to the human receptor n... -

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Basic information

Entry
Database: PDB / ID: 3sku
TitleHerpes simplex virus glycoprotein D bound to the human receptor nectin-1
Components
  • Glycoprotein D
  • Poliovirus receptor-related protein 1
KeywordsVIRAL PROTEIN/PROTEIN BINDING / Immunoglobulin-like fold / VIRAL PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


Nectin/Necl trans heterodimerization / desmosome organization / protein localization to cell junction / lens morphogenesis in camera-type eye / growth cone membrane / enamel mineralization / cell-cell contact zone / Adherens junctions interactions / virion binding / apical junction complex ...Nectin/Necl trans heterodimerization / desmosome organization / protein localization to cell junction / lens morphogenesis in camera-type eye / growth cone membrane / enamel mineralization / cell-cell contact zone / Adherens junctions interactions / virion binding / apical junction complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of synapse assembly / homophilic cell adhesion via plasma membrane adhesion molecules / coreceptor activity / presynaptic active zone membrane / cell adhesion molecule binding / hippocampal mossy fiber to CA3 synapse / axon guidance / adherens junction / cell-cell adhesion / retina development in camera-type eye / virus receptor activity / iron ion transport / carbohydrate binding / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / cell adhesion / immune response / symbiont entry into host cell / viral envelope / dendrite / protein-containing complex binding / virion membrane / protein homodimerization activity / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Glycoprotein D; Chain: A; / Glycoprotein D; Chain: A; - #10 / Nectin-1, first immunoglobulin (Ig) domain / Nectin-1, second immunoglobulin (Ig) domain / Herpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / : / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain ...Glycoprotein D; Chain: A; / Glycoprotein D; Chain: A; - #10 / Nectin-1, first immunoglobulin (Ig) domain / Nectin-1, second immunoglobulin (Ig) domain / Herpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / : / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Distorted Sandwich / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nectin-1 / Envelope glycoprotein D
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsDi Giovine, P. / Settembre, E.C. / Bhargava, A.K. / Luftig, M.A. / Lou, H. / Cohen, G.H. / Eisenberg, R.J. / Krummenacher, C. / Carfi, A.
CitationJournal: Plos Pathog. / Year: 2011
Title: Structure of herpes simplex virus glycoprotein d bound to the human receptor nectin-1.
Authors: Di Giovine, P. / Settembre, E.C. / Bhargava, A.K. / Luftig, M.A. / Lou, H. / Cohen, G.H. / Eisenberg, R.J. / Krummenacher, C. / Carfi, A.
History
DepositionJun 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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 6, 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: Glycoprotein D
B: Glycoprotein D
C: Glycoprotein D
E: Poliovirus receptor-related protein 1
D: Poliovirus receptor-related protein 1
F: Poliovirus receptor-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,07318
Polymers202,3486
Non-polymers4,72512
Water00
1
A: Glycoprotein D
D: Poliovirus receptor-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2686
Polymers67,4492
Non-polymers1,8194
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoprotein D
F: Poliovirus receptor-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9036
Polymers67,4492
Non-polymers1,4534
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycoprotein D
E: Poliovirus receptor-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9036
Polymers67,4492
Non-polymers1,4534
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.003, 188.003, 185.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12E
22D
32F
13E
23D
33F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUSERSER5AA28 - 25028 - 250
211LEULEUSERSER5BB28 - 25028 - 250
311LEULEUSERSER5CC28 - 25028 - 250
112PROPROLEULEU3ED146 - 241116 - 211
212PROPROLEULEU3DE146 - 241116 - 211
312PROPROLEULEU3FF146 - 241116 - 211
113VALVALASNASN5ED32 - 552 - 25
213VALVALASNASN5DE32 - 552 - 25
313VALVALASNASN5FF32 - 552 - 25
123GLNGLNLYSLYS5ED64 - 14534 - 115
223GLNGLNLYSLYS5DE64 - 14534 - 115
323GLNGLNLYSLYS5FF64 - 14534 - 115

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Glycoprotein D


Mass: 31624.973 Da / Num. of mol.: 3 / Fragment: UNP residues 26-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q991M3
#2: Protein Poliovirus receptor-related protein 1 / Herpes virus entry mediator C / Herpesvirus entry mediator C / HveC / Herpesvirus Ig-like receptor ...Herpes virus entry mediator C / Herpesvirus entry mediator C / HveC / Herpesvirus Ig-like receptor / HIgR / Nectin-1


Mass: 35824.211 Da / Num. of mol.: 3 / Fragment: UNP residues 31-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PVRL1, HVEC, PRR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15223
#3: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 4.66 Å3/Da / Density % sol: 73.63 %
Crystal growTemperature: 293 K / pH: 7.2
Details: 1.0 M Na2HPO4/KH2PO4 pH 7.2 and 300 mM NH4SO4, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 14, 2005
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.502
11-h,-k,l20.498
ReflectionResolution: 4→49.1 Å / Num. obs: 31947 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rsym value: 0.06 / Net I/σ(I): 8
Reflection shellResolution: 4→4.1 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.208 / % possible all: 99.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C36, 1NEU AND 3ALP

2c36

1neu

3alp


Resolution: 4→30 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.868 / SU B: 100.28 / SU ML: 0.561 / Cross valid method: THROUGHOUT / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1675 5.3 %RANDOM
Rwork0.266 ---
obs0.267 30227 98.9 %-
all-30529 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 151.77 Å2
Baniso -1Baniso -2Baniso -3
1-144.41 Å2-0 Å20 Å2
2--144.41 Å20 Å2
3----288.82 Å2
Refinement stepCycle: LAST / Resolution: 4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9592 0 310 0 9902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02210187
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.99413921
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.90551203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21923.372430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.664151560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2431572
X-RAY DIFFRACTIONr_chiral_restr0.0870.21607
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217671
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022009
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_it5.5271.56108
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it8.41229962
X-RAY DIFFRACTIONr_scbond_it14.48534079
X-RAY DIFFRACTIONr_scangle_it20.54.53958
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
21E268tight positional0.40.05
22D268tight positional0.380.05
23F268tight positional0.450.05
11A892medium positional0.040.5
12B892medium positional0.040.5
13C892medium positional0.040.5
31E424medium positional0.370.5
32D424medium positional0.480.5
33F424medium positional0.40.5
11A863loose positional0.045
12B863loose positional0.045
13C863loose positional0.045
21E263loose positional0.535
22D263loose positional0.535
23F263loose positional0.595
31E410loose positional0.695
32D410loose positional0.645
33F410loose positional0.65
21E268tight thermal0.5
22D268tight thermal0.5
23F268tight thermal0.5
11A892medium thermal2
12B892medium thermal2
13C892medium thermal2
31E424medium thermal2
32D424medium thermal2
33F424medium thermal2
11A863loose thermal10
12B863loose thermal10
13C863loose thermal10
21E263loose thermal10
22D263loose thermal10
23F263loose thermal10
31E410loose thermal10
32D410loose thermal10
33F410loose thermal10
LS refinement shellResolution: 4→4.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 120 -
Rwork0.364 2113 -
obs--97.13 %
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)
12.59710.406-1.32562.9672-0.06046.5841-0.2135-0.33740.12530.05240.18090.05530.1966-0.93520.03260.50430.1303-0.09961.1714-0.01542.0126-33.072811.2552-4.0519
22.3719-0.802-0.31364.06010.92955.78960.09970.00970.14480.0007-0.2643-0.17350.2641.42240.16460.3121-0.20460.02561.5761-0.20952.0836-60.5254-46.8905-26.493
33.0568-0.4763-0.6512.3554-0.06145.9792-0.3264-0.18730.1049-0.07550.2539-0.1995-1.3891-0.25560.07251.43710.0896-0.00180.25330.02272.0342-96.3909-18.779827.3524
41.50530.8662-4.253618.3684-2.02027.83810.35610.4177-0.1623-0.4612-0.03410.1072-0.53550.0802-0.32210.3452-0.23060.0436-0.0093-0.16081.7686-88.9782-37.58649.4006
59.3904-5.0718-2.34574.21521.76987.52980.27240.3998-0.7625-0.6788-0.476-0.00220.26190.44620.20360.22140.0436-0.12240.02420.03651.5058-12.64212.2465-21.5267
611.29833.6051-3.03124.15022.50185.2430.5208-0.42660.0981.12810.03150.09320.79110.6931-0.55230.3078-0.3192-0.05440.2788-0.25431.7654-82.0784-43.504-9.8081
70.17932.62960.44127.2469-3.45812.72010.23980.32960.1238-1.15310.5867-0.18010.3841-0.3315-0.82651.5225-0.4065-0.37820.2515-0.04841.9885-99.5805-73.64036.5612
810.8412-2.6642-3.30135.48734.7619.68230.28290.65690.0625-0.5622-0.31950.37780.78280.90250.03660.84310.8184-0.16040.75890.10811.681515.6935-11.9636-24.5265
912.23951.5672-10.77161.0477-3.04599.77830.48880.9280.31420.3645-0.0772-0.08720.9171-1.5614-0.41151.1821-1.261-0.2240.97010.16911.8355-112.3536-64.0345-5.3454
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 252
2X-RAY DIFFRACTION2B28 - 250
3X-RAY DIFFRACTION3C23 - 250
4X-RAY DIFFRACTION4E32 - 145
5X-RAY DIFFRACTION5D32 - 145
6X-RAY DIFFRACTION6F32 - 145
7X-RAY DIFFRACTION7E146 - 241
8X-RAY DIFFRACTION8D146 - 241
9X-RAY DIFFRACTION9F146 - 241

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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