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- PDB-9rm2: BKPyV VP1 IN COMPLEX WITH 319C07-FAB -

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Basic information

Entry
Database: PDB / ID: 9rm2
TitleBKPyV VP1 IN COMPLEX WITH 319C07-FAB
Components
  • (319C07 antibody ...) x 2
  • Major capsid protein VP1
KeywordsVIRAL PROTEIN / FAB ANTIBODY BKPyV VP1 virus capsid
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / TRIETHYLENE GLYCOL / Major capsid protein VP1
Similarity search - Component
Biological speciesHomo sapiens (human)
Betapolyomavirus hominis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsSchmitt, S. / Hillenbrand, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A Highly Potent Human Antibody Neutralizing All Serotypes of BK Polyomavirus
Authors: Weber, M. / Hillenbrand, M.
History
DepositionJun 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 319C07 antibody heavy chain, Fab fragment
L: 319C07 antibody light chain, Fab fragment
P: Major capsid protein VP1
A: 319C07 antibody heavy chain, Fab fragment
B: 319C07 antibody light chain, Fab fragment
C: Major capsid protein VP1
D: 319C07 antibody heavy chain, Fab fragment
E: 319C07 antibody light chain, Fab fragment
F: Major capsid protein VP1
G: 319C07 antibody heavy chain, Fab fragment
J: 319C07 antibody light chain, Fab fragment
K: Major capsid protein VP1
M: 319C07 antibody heavy chain, Fab fragment
N: 319C07 antibody light chain, Fab fragment
O: Major capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)408,45375
Polymers402,35715
Non-polymers6,09660
Water38,8402156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area69340 Å2
ΔGint-193 kcal/mol
Surface area134080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.349, 172.078, 113.144
Angle α, β, γ (deg.)90.00, 97.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11H
21A
12H
22D
13H
23G
14H
24M
15L
25B
16L
26E
17L
27J
18L
28N
19P
29C
110P
210F
111P
211K
112P
212O
113A
213D
114A
214G
115A
215M
116B
216E
117B
217J
118B
218N
119C
219F
120C
220K
121C
221O
122D
222G
123D
223M
124E
224J
125E
225N
126F
226K
127F
227O
128G
228M
129J
229N
130K
230O

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLUGLUHA1 - 2201 - 220
21GLNGLNGLUGLUAD1 - 2201 - 220
12GLNGLNPROPROHA1 - 2211 - 221
22GLNGLNPROPRODG1 - 2211 - 221
13GLNGLNPROPROHA1 - 2211 - 221
23GLNGLNPROPROGJ1 - 2211 - 221
14GLNGLNPROPROHA1 - 2211 - 221
24GLNGLNPROPROMM1 - 2211 - 221
15GLUGLUASNASNLB1 - 2111 - 211
25GLUGLUASNASNBE1 - 2111 - 211
16GLUGLUARGARGLB1 - 2121 - 212
26GLUGLUARGARGEH1 - 2121 - 212
17GLUGLUASNASNLB1 - 2111 - 211
27GLUGLUASNASNJK1 - 2111 - 211
18GLUGLUASNASNLB1 - 2111 - 211
28GLUGLUASNASNNN1 - 2111 - 211
19LEULEUASNASNPC2 - 27327 - 298
29LEULEUASNASNCF2 - 27327 - 298
110LEULEUASNASNPC2 - 27327 - 298
210LEULEUASNASNFI2 - 27327 - 298
111LEULEUPROPROPC3 - 27428 - 299
211LEULEUPROPROKL3 - 27428 - 299
112LEULEUPROPROPC3 - 27428 - 299
212LEULEUPROPROOO3 - 27428 - 299
113GLNGLNSERSERAD1 - 2231 - 223
213GLNGLNSERSERDG1 - 2231 - 223
114GLNGLNLYSLYSAD1 - 2221 - 222
214GLNGLNLYSLYSGJ1 - 2221 - 222
115GLNGLNLYSLYSAD1 - 2221 - 222
215GLNGLNLYSLYSMM1 - 2221 - 222
116GLUGLUASNASNBE1 - 2111 - 211
216GLUGLUASNASNEH1 - 2111 - 211
117GLUGLUGLYGLYBE1 - 2131 - 213
217GLUGLUGLYGLYJK1 - 2131 - 213
118GLUGLUGLYGLYBE1 - 2131 - 213
218GLUGLUGLYGLYNN1 - 2131 - 213
119LEULEUASNASNCF2 - 27327 - 298
219LEULEUASNASNFI2 - 27327 - 298
120LEULEUASNASNCF3 - 27328 - 298
220LEULEUASNASNKL3 - 27328 - 298
121LEULEUASNASNCF3 - 27328 - 298
221LEULEUASNASNOO3 - 27328 - 298
122GLNGLNPROPRODG1 - 2211 - 221
222GLNGLNPROPROGJ1 - 2211 - 221
123GLNGLNPROPRODG1 - 2211 - 221
223GLNGLNPROPROMM1 - 2211 - 221
124GLUGLUASNASNEH1 - 2111 - 211
224GLUGLUASNASNJK1 - 2111 - 211
125GLUGLUASNASNEH1 - 2111 - 211
225GLUGLUASNASNNN1 - 2111 - 211
126LEULEUASNASNFI3 - 27328 - 298
226LEULEUASNASNKL3 - 27328 - 298
127LEULEUASNASNFI3 - 27328 - 298
227LEULEUASNASNOO3 - 27328 - 298
128GLNGLNLYSLYSGJ1 - 2221 - 222
228GLNGLNLYSLYSMM1 - 2221 - 222
129GLUGLUGLUGLUJK1 - 2141 - 214
229GLUGLUGLUGLUNN1 - 2141 - 214
130LEULEUTYRTYRKL3 - 27528 - 300
230LEULEUTYRTYROO3 - 27528 - 300

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

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Components

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Protein , 1 types, 5 molecules PCFKO

#3: Protein
Major capsid protein VP1 / Major structural protein VP1


Mass: 32965.383 Da / Num. of mol.: 5 / Mutation: C105S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betapolyomavirus hominis / Production host: Escherichia coli (E. coli) / References: UniProt: P03088

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Antibody , 2 types, 10 molecules HADGMLBEJN

#1: Antibody
319C07 antibody heavy chain, Fab fragment


Mass: 24208.133 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
319C07 antibody light chain, Fab fragment


Mass: 23297.867 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 9 types, 2216 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O4
#9: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#11: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2156 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MIB buffer pH 4.75, 21% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jun 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.957→91.87 Å / Num. obs: 295460 / % possible obs: 99.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 8.5
Reflection shellResolution: 1.957→1.991 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 295460 / Rsym value: 1.22 / % possible all: 98.7

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Processing

Software
NameVersionClassification
autoPROCdata reduction
XDS(VERSION Jan 31data reduction
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→91.87 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.55 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21819 13696 5 %RANDOM
Rwork0.18738 ---
obs0.18892 261412 92.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.491 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å2-0 Å2-0.77 Å2
2---0.42 Å2-0 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.96→91.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27059 0 391 2156 29606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01327883
X-RAY DIFFRACTIONr_bond_other_d0.0020.01725648
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.64837908
X-RAY DIFFRACTIONr_angle_other_deg1.141.56959153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.56653569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97122.5281238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.451154190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.32915132
X-RAY DIFFRACTIONr_chiral_restr0.0520.23650
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0231627
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026289
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_it1.8224.11214159
X-RAY DIFFRACTIONr_mcbond_other1.8224.11214158
X-RAY DIFFRACTIONr_mcangle_it2.9456.15317692
X-RAY DIFFRACTIONr_mcangle_other2.9446.15417693
X-RAY DIFFRACTIONr_scbond_it1.9364.19613724
X-RAY DIFFRACTIONr_scbond_other1.9364.19713725
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1016.20720192
X-RAY DIFFRACTIONr_long_range_B_refined4.97645.93228760
X-RAY DIFFRACTIONr_long_range_B_other4.90645.6828454
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11H22350.02
12A22350.02
21H22200.01
22D22200.01
31H22010.03
32G22010.03
41H22490.02
42M22490.02
51L22720.03
52B22720.03
61L22310.02
62E22310.02
71L22780.02
72J22780.02
81L22820.02
82N22820.02
91P29090.03
92C29090.03
101P29040.02
102F29040.02
111P29890.03
112K29890.03
121P29910.03
122O29910.03
131A23040.02
132D23040.02
141A22670.03
142G22670.03
151A23180.03
152M23180.03
161B22140.03
162E22140.03
171B22940.02
172J22940.02
181B23110.02
182N23110.02
191C29350.03
192F29350.03
201C29300.03
202K29300.03
211C28990.03
212O28990.03
221D22730.03
222G22730.03
231D23260.03
232M23260.03
241E22120.03
242J22120.03
251E22340.02
252N22340.02
261F29330.02
262K29330.02
271F29180.03
272O29180.03
281G23240.03
282M23240.03
291J23270.02
292N23270.02
301K30060.02
302O30060.02
LS refinement shellResolution: 1.96→2.008 Å
RfactorNum. reflection% reflection
Rfree0.309 1092 -
Rwork-19498 -
obs--94.12 %

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