[English] 日本語
Yorodumi
- PDB-5vic: Crystal structure of anti-Zika antibody Z004 bound to DENV-1 Enve... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vic
TitleCrystal structure of anti-Zika antibody Z004 bound to DENV-1 Envelope protein DIII
Components
  • Dengue 1 Envelope DIII domain
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
KeywordsIMMUNE SYSTEM / antibody / Fab / Zika / Dengue / recurrent / neutralizing
Function / homology
Function and homology information


immunoglobulin complex / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding ...immunoglobulin complex / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / : / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / adaptive immune response / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus ...Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Helicase superfamily 1/2, ATP-binding domain / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa light chain / Genome polyprotein / Envelope protein / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Dengue virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsKeeffe, J.R. / West Jr., A.P. / Gristick, H.B. / Bjorkman, P.J.
CitationJournal: Cell / Year: 2017
Title: Recurrent Potent Human Neutralizing Antibodies to Zika Virus in Brazil and Mexico.
Authors: Robbiani, D.F. / Bozzacco, L. / Keeffe, J.R. / Khouri, R. / Olsen, P.C. / Gazumyan, A. / Schaefer-Babajew, D. / Avila-Rios, S. / Nogueira, L. / Patel, R. / Azzopardi, S.A. / Uhl, L.F.K. / ...Authors: Robbiani, D.F. / Bozzacco, L. / Keeffe, J.R. / Khouri, R. / Olsen, P.C. / Gazumyan, A. / Schaefer-Babajew, D. / Avila-Rios, S. / Nogueira, L. / Patel, R. / Azzopardi, S.A. / Uhl, L.F.K. / Saeed, M. / Sevilla-Reyes, E.E. / Agudelo, M. / Yao, K.H. / Golijanin, J. / Gristick, H.B. / Lee, Y.E. / Hurley, A. / Caskey, M. / Pai, J. / Oliveira, T. / Wunder, E.A. / Sacramento, G. / Nery, N. / Orge, C. / Costa, F. / Reis, M.G. / Thomas, N.M. / Eisenreich, T. / Weinberger, D.M. / de Almeida, A.R.P. / West, A.P. / Rice, C.M. / Bjorkman, P.J. / Reyes-Teran, G. / Ko, A.I. / MacDonald, M.R. / Nussenzweig, M.C.
History
DepositionApr 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain
E: Dengue 1 Envelope DIII domain


Theoretical massNumber of molelcules
Total (without water)59,3273
Polymers59,3273
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-31 kcal/mol
Surface area23500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.225, 74.225, 190.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 24984.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) / References: UniProt: S6B291
#2: Antibody Fab light chain / Fragment antigen-binding / Immunoglobulin kappa light chain EU


Mass: 23552.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) / References: UniProt: P0DOX7
#3: Protein Dengue 1 Envelope DIII domain


Mass: 10790.247 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus type 1 (strain Nauru/West Pac/1974)
Strain: Nauru/West Pac/1974 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17763, UniProt: Q8BE39*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M sodium acetate trihydrate pH 4.5, 30% w/v PEG 1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2017
RadiationMonochromator: double crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→74.23 Å / Num. obs: 15181 / % possible obs: 98.6 % / Redundancy: 10.9 % / Biso Wilson estimate: 58.66 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.235 / Rpim(I) all: 0.073 / Rrim(I) all: 0.247 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.7-2.8310.81.7670.5770.5541.85599.6
8.96-74.239.50.0580.9980.0190.06197.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.7 Å69.17 Å
Translation4.7 Å69.17 Å

-
Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHASER2.7.16phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→37.113 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9
RfactorNum. reflection% reflection
Rfree0.2858 520 4.66 %
Rwork0.2346 --
obs0.2369 11151 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 239.75 Å2 / Biso mean: 59.0363 Å2 / Biso min: 30.71 Å2
Refinement stepCycle: final / Resolution: 3→37.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 0 0 3904
Num. residues----513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033995
X-RAY DIFFRACTIONf_angle_d0.6335426
X-RAY DIFFRACTIONf_chiral_restr0.044615
X-RAY DIFFRACTIONf_plane_restr0.004687
X-RAY DIFFRACTIONf_dihedral_angle_d12.6192395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.30170.33121400.296226022742100
3.3017-3.77910.32271250.25542586271197
3.7791-4.75970.29171280.21062631275998
4.7597-37.11550.24051270.22222812293999
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)
11.1202-0.759-0.55645.7293.5735.6750.15690.04920.2434-0.81070.6195-0.5881-1.08130.9666-0.70470.5086-0.03090.21380.65490.11350.49841.434464.3723233.2686
26.64610.7107-0.1715.81020.6736.9824-0.21130.0197-0.3201-0.24640.3623-0.7448-0.73850.2033-0.06850.29840.01980.07230.25290.01190.34238.951362.0395245.5396
33.3841-1.8226-1.00362.19971.42516.42710.093-0.45060.09940.18560.1401-0.42890.38880.646-0.16740.3269-0.06230.07560.41690.03540.472439.16760.0937241.9885
42.7709-2.36361.20363.8484-2.21953.4141-0.4847-0.00530.17470.1060.24020.1912-0.13210.07270.23920.4558-0.1445-0.01460.34630.00570.393725.858773.4815218.9861
50.97450.5646-0.30726.00651.08026.7138-0.43270.51890.3798-1.2157-0.320.5218-2.4549-0.60780.10321.2622-0.1003-0.33380.39120.11390.908220.807686.2615215.6826
64.7818-4.92532.42746.1988-1.31922.7289-0.52730.20231.6292-0.02350.0461-0.7682-0.81530.32280.48160.6678-0.17290.0190.52360.03470.572630.962578.9795212.8074
73.78651.7832-0.01322.750.22374.37860.06690.09850.0407-0.3491-0.27950.1438-0.2329-1.04150.21950.47590.11030.07930.4935-0.09890.375120.245468.7251250.4377
81.28870.32651.48420.97510.19823.6298-0.3174-0.08430.33520.00460.09370.1603-0.7479-0.4330.19130.45420.1397-0.00620.3983-0.04410.504916.893472.1319235.1278
94.0424-1.02432.61652.2111.89389.0774-0.5230.007-0.13180.40130.04320.56450.7161-1.35740.54780.6598-0.2226-0.00710.5989-0.05030.55555.526669.0893216.9111
106.5644-1.0877-2.66923.0257-0.33836.14-0.42270.47850.5228-0.03980.00510.10240.1708-0.33280.32390.455-0.0263-0.08760.22180.04270.547911.397673.3575215.5617
113.91040.0021-0.17962.4136-0.84494.7417-1.15120.18980.9796-0.41550.49590.1515-0.5212-2.5983-0.01110.76070.0005-0.27921.11810.22350.66881.628977.8977214.9984
128.1065-7.3318-6.24829.83337.06815.8859-1.0574-1.7101-0.9396-0.71190.63320.75490.13492.07040.18650.5967-0.0485-0.01130.81270.10510.561737.631451.7435259.4402
135.7566-1.54841.55632.49861.19371.6221-0.5012-1.6001-0.0340.3138-0.50850.45320.7408-1.26280.77120.89720.19230.3961.20120.11250.926136.390752.2815275.034
142.84280.3765-0.70825.0198-1.11160.48850.21880.6428-0.4860.4448-0.1068-1.1386-0.0250.57760.07530.5741-0.0010.05550.82710.13030.634339.944653.0894261.7473
153.7078-0.3581-0.42691.16730.99453.129-0.5235-0.10671.0349-0.00270.1689-0.14281.09230.34870.19641.27410.2356-0.01220.76490.18451.147538.441845.8577265.9556
162.4264-3.2466-3.14335.31265.47757.40970.2547-1.27690.3595-0.42910.7413-1.61190.25541.5249-0.3480.7848-0.0342-0.10031.27070.16520.915944.862955.3708275.4748
178.1360.36572.2997.0353-4.53039.2344-0.8719-3.04170.96671.9670.63350.8417-2.1972-0.6260.34880.81070.26610.0910.9565-0.08610.811738.402662.0114269.0944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 23 )H1 - 23
2X-RAY DIFFRACTION2chain 'H' and (resid 24 through 60 )H24 - 60
3X-RAY DIFFRACTION3chain 'H' and (resid 61 through 111 )H61 - 111
4X-RAY DIFFRACTION4chain 'H' and (resid 112 through 184 )H112 - 184
5X-RAY DIFFRACTION5chain 'H' and (resid 185 through 203 )H185 - 203
6X-RAY DIFFRACTION6chain 'H' and (resid 204 through 214 )H204 - 214
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 61 )L1 - 61
8X-RAY DIFFRACTION8chain 'L' and (resid 62 through 139 )L62 - 139
9X-RAY DIFFRACTION9chain 'L' and (resid 140 through 160 )L140 - 160
10X-RAY DIFFRACTION10chain 'L' and (resid 161 through 197 )L161 - 197
11X-RAY DIFFRACTION11chain 'L' and (resid 198 through 211 )L198 - 211
12X-RAY DIFFRACTION12chain 'E' and (resid 298 through 307 )E298 - 307
13X-RAY DIFFRACTION13chain 'E' and (resid 308 through 327 )E308 - 327
14X-RAY DIFFRACTION14chain 'E' and (resid 328 through 340 )E328 - 340
15X-RAY DIFFRACTION15chain 'E' and (resid 351 through 364 )E351 - 364
16X-RAY DIFFRACTION16chain 'E' and (resid 365 through 376 )E365 - 376
17X-RAY DIFFRACTION17chain 'E' and (resid 377 through 391 )E377 - 391

+
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