[English] 日本語
Yorodumi
- PDB-4gjt: complex structure of nectin-4 bound to MV-H -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gjt
Titlecomplex structure of nectin-4 bound to MV-H
Components
  • Hemagglutinin glycoprotein
  • Poliovirus receptor-related protein 4
KeywordsMEMBRANE PROTEIN/VIRAL PROTEIN / six-bladed -propeller / IgV-like fold / viral entry / MV-H / nectin-4 / beta4/beta5 groove / MEMBRANE PROTEIN-VIRAL PROTEIN complex
Function / homology
Function and homology information


Nectin/Necl trans heterodimerization / Adherens junctions interactions / negative regulation of natural killer cell mediated cytotoxicity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / adherens junction / virus receptor activity / host cell surface receptor binding / receptor ligand activity / viral envelope ...Nectin/Necl trans heterodimerization / Adherens junctions interactions / negative regulation of natural killer cell mediated cytotoxicity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / adherens junction / virus receptor activity / host cell surface receptor binding / receptor ligand activity / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Nectin-4 / : / : / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller ...Nectin-4 / : / : / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Hemagglutinin glycoprotein / Nectin-4
Similarity search - Component
Biological speciesMeasles virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1001 Å
AuthorsZhang, X. / Lu, G. / Qi, J. / Li, Y. / He, Y. / Xu, X. / Shi, J. / Zhang, C. / Yan, J. / Gao, G.F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Structure of measles virus hemagglutinin bound to its epithelial receptor nectin-4
Authors: Zhang, X. / Lu, G. / Qi, J. / Li, Y. / He, Y. / Xu, X. / Shi, J. / Zhang, C.W. / Yan, J. / Gao, G.F.
History
DepositionAug 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin glycoprotein
B: Poliovirus receptor-related protein 4
C: Poliovirus receptor-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8704
Polymers79,6493
Non-polymers2211
Water1,42379
1
A: Hemagglutinin glycoprotein
B: Poliovirus receptor-related protein 4
hetero molecules

A: Hemagglutinin glycoprotein
B: Poliovirus receptor-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,6086
Polymers132,1664
Non-polymers4422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6300 Å2
ΔGint-44 kcal/mol
Surface area46680 Å2
MethodPISA
2
C: Poliovirus receptor-related protein 4


Theoretical massNumber of molelcules
Total (without water)13,5661
Polymers13,5661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.350, 171.778, 117.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Hemagglutinin glycoprotein


Mass: 52516.715 Da / Num. of mol.: 1 / Fragment: MV-H fragment, 156-617
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles virus / Strain: Ichinose-B95a / Gene: H, hemagglutinin / Plasmid: pFast-bac1 / Cell line (production host): HIFIVE INSECT CELLS / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q786F2
#2: Protein Poliovirus receptor-related protein 4 / Ig superfamily receptor LNIR / Nectin-4 / Processed poliovirus receptor-related protein 4


Mass: 13566.088 Da / Num. of mol.: 2 / Fragment: nectin-4 fragment, 32-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LNIR, nectin-4, PRR4, PVRL4 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q96NY8
#3: 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.: 1
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M Magnesium formate dehydrate, 15%(w/v) Polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 15515 / Num. obs: 15494 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 25.43
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 7 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 3.522 / Num. unique all: 1525 / Rsym value: 0.548 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RKC and 3U83

2rkc

3u83


Resolution: 3.1001→37.129 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2778 774 5 %Random
Rwork0.2604 ---
obs0.2613 15471 99.9 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.289 Å2 / ksol: 0.288 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2708 Å20 Å2-0 Å2
2--1.2376 Å2-0 Å2
3---0.0332 Å2
Refinement stepCycle: LAST / Resolution: 3.1001→37.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4927 0 14 79 5020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085064
X-RAY DIFFRACTIONf_angle_d1.086876
X-RAY DIFFRACTIONf_dihedral_angle_d19.4541846
X-RAY DIFFRACTIONf_chiral_restr0.079761
X-RAY DIFFRACTIONf_plane_restr0.007895
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.1001-3.29420.32111370.31962413
3.2942-3.54840.31211340.29672402
3.5484-3.90510.33351330.27892409
3.9051-4.46940.25451230.24452439
4.4694-5.62780.26211090.21942492
5.6278-37.13160.25311380.26342542
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)
13.7513-0.38680.03883.2557-1.22744.6601-0.08090.05750.0788-0.18780.25430.00550.0097-0.1913-0.12810.2145-0.0023-0.01880.21730.0150.3514-16.4162-10.18693.3892
22.8750.174-1.30592.8319-0.32974.4057-0.3968-0.3122-0.2154-0.0730.0660.35751.06620.0720.15650.46960.06120.11580.35380.01770.4637-5.8248-26.09581.9151
31.3559-0.5621.88270.2318-0.71542.6897-0.17570.3442-1.97681.12670.0426-1.15051.25890.56250.33881.23740.21930.27530.35930.10651.3307-9.3588-40.309716.574
44.6008-1.356-2.35941.93410.04724.7853-0.49620.717-1.61360.2272-0.4212.03441.6987-1.0029-0.29991.2089-0.22020.20150.5117-0.02751.082-17.5202-39.86515.1084
52.70570.3696-1.36781.52790.36872.5075-0.1833-0.5806-0.33730.2685-0.07020.27680.86210.51560.2230.62340.18320.0670.29840.04810.3965-8.8111-29.179519.2118
62.6764-2.2561-0.35533.2082-0.83484.7146-0.01840.3744-0.559-0.03580.26150.43820.9923-0.1621-0.24650.4783-0.0647-0.00060.39430.02010.4497-26.3288-21.207521.4357
72.92710.0326-1.4874.1509-0.2752.28-0.19670.31310.2632-0.18760.23290.4556-0.5569-0.12650.05660.4610.017-0.07990.54570.10750.4801-27.349-12.658317.2814
84.54380.09512.02625.48990.95357.23-0.23390.33840.2654-0.4628-0.26170.803-0.21040.13850.11390.28890.02460.02130.46030.0710.4453-29.2328-12.832110.919
92.5618-0.6892-3.89992.5269-0.92827.5642-0.3196-2.1724-0.23970.81070.89630.2773-0.9469-0.5091-0.19820.8835-0.12690.17091.2166-0.10630.6515-28.193-19.109743.0731
101.7268-0.0935-0.06150.05560.04840.0379-0.0105-1.4739-0.85321.73430.32820.71010.4892-0.89340.67451.56450.13830.45051.50230.7130.9383-30.5982-30.105356.605
113.54390.6369-1.75864.56491.8988.0256-0.05360.27380.235-0.4268-0.4970.92290.5165-0.7424-0.41020.6012-0.07490.01221.1635-0.04230.4253-32.3496-22.41834.1293
122.9054-2.24381.21013.6115-2.94313.35650.5215-0.3262-0.13340.2385-0.2463-0.72570.14430.36390.3821.032-0.1159-0.24370.74390.39410.7957-23.3789-31.229140.7652
134.90052.11832.16.83065.51454.49490.4331-0.9849-0.44931.12240.4057-0.43470.50180.3991-0.40541.17960.05150.23431.66650.36271.5458-11.8506-30.832450.2252
146.3578-1.4052-2.59985.25130.09674.61560.58081.7444-1.52991.35670.1143-0.43960.9646-0.8809-0.16020.9529-0.0096-0.07141.11790.33710.9063-24.8812-38.85237.9314
150.54370.14590.97731.4454-0.76112.47190.3247-0.3587-1.53120.91390.02510.01760.9151-0.7082-0.22951.3034-0.10950.14781.22560.43381.055-31.2978-36.053545.1142
160.3820.569-0.23041.7715-0.5530.22361.1811-0.861-0.96030.63270.0084-0.91930.5493-0.61931.30220.9937-0.0247-0.19830.95250.46430.8138-22.7357-29.069345.4867
170.56491.2833-0.83761.9296-0.96747.84110.8125-1.0166-0.0832.7819-0.5921-0.84740.446-0.06520.16740.5567-0.32480.18371.40620.23170.8865-22.6094-23.631548.3694
182.30061.7044-0.05424.2071-0.07072.1950.144-0.75060.20431.7172-0.10840.42410.7426-0.0772-0.09580.6597-0.00170.11490.8644-0.23820.36375.2036-22.6499-9.9426
195.3551-0.7191-3.77742.878-4.65261.9716-0.15740.9935-0.6055-0.03490.65091.17124.0031-1.4776-0.06021.50450.04110.15070.50390.07670.779-7.2039-33.1477-15.6199
203.8782-0.14320.85263.39861.1656.33340.0858-0.03290.206-0.92630.29180.18281.57270.0031-0.06771.0817-0.15050.15830.65260.00470.38021.9988-27.8362-22.621
210.0059-0.0484-0.11781.9492.53084.1242-0.2258-0.04390.3128-0.58620.91120.1306-0.52460.2404-0.29721.0583-0.7575-0.09881.95640.14251.12316.8737-11.3306-25.9395
225.98431.1891.62913.55742.14911.4489-0.97440.74130.4435-1.25541.2457-0.47430.45472.0817-0.59991.34170.2236-0.01271.20130.01560.27857.3879-27.1672-25.4618
234.8943.20930.76536.3456-2.52292.7225-0.92050.7245-0.9966-0.4541.0379-0.30452.49151.15870.03381.27070.55540.17611.3636-0.25960.51457.4894-35.6503-26.9643
243.27672.7391-1.71452.8204-1.49270.9135-0.12850.0876-0.05560.22151.3157-0.04242.06322.6035-0.08541.06790.4879-0.231.8054-0.32250.809815.3471-26.9609-21.2048
251.1406-0.4775-0.10130.20620.08620.2761-0.0384-0.046-0.14780.08590.0687-0.18070.08170.0278-0.04992.37641.17821.09481.18710.70371.80777.6685-38.5296-12.1768
267.76351.14810.44555.9045-0.30275.68850.12940.32860.6864-0.56160.0549-1.22831.05881.18850.0240.87950.35850.19781.10950.13370.800610.0752-25.3219-14.4048
276.54852.77843.52035.74021.53113.7719-0.26831.26660.39-1.3341-0.1629-0.9021-0.19230.0925-0.44660.9903-0.11920.18230.7735-0.13470.3619-0.6266-24.1811-21.7693
289.17572.25991.38326.5669-0.19055.3168-0.06130.87651.421-0.7571-0.10860.4971-0.18441.30280.06020.83760.19130.33660.76230.24890.6702-3.0709-21.9929-19.1796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 156:300)
2X-RAY DIFFRACTION2chain A and (resseq 301:361)
3X-RAY DIFFRACTION3chain A and (resseq 362:385)
4X-RAY DIFFRACTION4chain A and (resseq 386:416)
5X-RAY DIFFRACTION5chain A and (resseq 417:494)
6X-RAY DIFFRACTION6chain A and (resseq 495:543)
7X-RAY DIFFRACTION7chain A and (resseq 544:575)
8X-RAY DIFFRACTION8chain A and (resseq 576:606)
9X-RAY DIFFRACTION9chain B and (resseq 1:7)
10X-RAY DIFFRACTION10chain B and (resseq 8:19)
11X-RAY DIFFRACTION11chain B and (resseq 20:30)
12X-RAY DIFFRACTION12chain B and (resseq 31:38)
13X-RAY DIFFRACTION13chain B and (resseq 39:46)
14X-RAY DIFFRACTION14chain B and (resseq 47:60)
15X-RAY DIFFRACTION15chain B and (resseq 61:84)
16X-RAY DIFFRACTION16chain B and (resseq 85:104)
17X-RAY DIFFRACTION17chain B and (resseq 105:114)
18X-RAY DIFFRACTION18chain C and (resseq 1:19)
19X-RAY DIFFRACTION19chain C and (resseq 20:29)
20X-RAY DIFFRACTION20chain C and (resseq 30:38)
21X-RAY DIFFRACTION21chain C and (resseq 39:45)
22X-RAY DIFFRACTION22chain C and (resseq 46:52)
23X-RAY DIFFRACTION23chain C and (resseq 53:59)
24X-RAY DIFFRACTION24chain C and (resseq 60:69)
25X-RAY DIFFRACTION25chain C and (resseq 70:74)
26X-RAY DIFFRACTION26chain C and (resseq 75:91)
27X-RAY DIFFRACTION27chain C and (resseq 92:101)
28X-RAY DIFFRACTION28chain C and (resseq 102:112)

+
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