[English] 日本語
Yorodumi
- PDB-7wvd: Crystal structure of H14 complexed with SIA28 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wvd
TitleCrystal structure of H14 complexed with SIA28
Components
  • (Hemagglutinin) x 2
  • Heavy chain of SIA28
  • Light chain of SIA28
KeywordsVIRUS / Influenza Virus / Hemagglutinin / Monoclonal Antibody
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins ...Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.39 Å
AuthorsChen, Y. / Qi, J. / Gao, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for a human broadly neutralizing influenza A hemagglutinin stem-specific antibody including H17/18 subtypes.
Authors: Chen, Y. / Wang, F. / Yin, L. / Jiang, H. / Lu, X. / Bi, Y. / Zhang, W. / Shi, Y. / Burioni, R. / Tong, Z. / Song, H. / Qi, J. / Gao, G.F.
History
DepositionFeb 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
G: Heavy chain of SIA28
H: Light chain of SIA28
I: Heavy chain of SIA28
J: Light chain of SIA28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,78415
Polymers213,86510
Non-polymers1,9195
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42040 Å2
ΔGint-178 kcal/mol
Surface area73540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.662, 120.990, 129.759
Angle α, β, γ (deg.)90.000, 107.730, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin


Mass: 34784.203 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/mallard/Wisconsin/10OS3941/2010(H14N6) / Gene: HA / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: L7YN49
#2: Protein Hemagglutinin


Mass: 19922.895 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A5C1ZLI8

-
Antibody , 2 types, 4 molecules GIHJ

#3: Antibody Heavy chain of SIA28


Mass: 13501.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Antibody Light chain of SIA28


Mass: 11370.739 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

-
Sugars , 2 types, 5 molecules

#5: 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.: 4
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
#6: 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: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris 5 % w/v PGA-LM 20 % w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.39→50 Å / Num. obs: 36855 / % possible obs: 98.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 61.99 Å2 / CC1/2: 0.963 / Net I/σ(I): 5.6
Reflection shellResolution: 3.4→3.52 Å / Num. unique obs: 3591 / CC1/2: 0.509

-
Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eyj

3eyj


Resolution: 3.39→49.72 Å / SU ML: 0.4499 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.886
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2614 1615 4.95 %
Rwork0.2212 31022 -
obs0.2232 32637 86.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.55 Å2
Refinement stepCycle: LAST / Resolution: 3.39→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15000 0 126 0 15126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315436
X-RAY DIFFRACTIONf_angle_d0.585420929
X-RAY DIFFRACTIONf_chiral_restr0.0532328
X-RAY DIFFRACTIONf_plane_restr0.00422729
X-RAY DIFFRACTIONf_dihedral_angle_d14.26775628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.39-3.490.38610.32831047X-RAY DIFFRACTION35.82
3.49-3.60.42081040.29981628X-RAY DIFFRACTION56.07
3.6-3.730.29761290.27322152X-RAY DIFFRACTION73.58
3.73-3.880.33771470.27672571X-RAY DIFFRACTION87.06
3.88-4.060.30361320.26322837X-RAY DIFFRACTION95.16
4.06-4.270.29981340.23392907X-RAY DIFFRACTION97.97
4.27-4.540.25041520.20612942X-RAY DIFFRACTION98.72
4.54-4.890.24691580.19452958X-RAY DIFFRACTION99.3
4.89-5.380.22951560.18832970X-RAY DIFFRACTION99.74
5.38-6.160.26171490.20452970X-RAY DIFFRACTION99.65
6.16-7.750.2181460.20782993X-RAY DIFFRACTION99.71
7.76-49.720.18551470.18973047X-RAY DIFFRACTION99.41
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)
11.21026450798-0.134576861795-0.6277536099520.4161643907150.03723900559870.930634087595-0.00621896692019-0.09378511965990.100703120009-0.06205464736840.0404964482364-0.119366235260.1802443584560.281018928401-0.06491112697220.2660563883670.0439468473613-0.02926667921910.241101036806-0.01209042270010.3001774410694.93328781736-1.8090707372719.4895579595
20.6811574824320.0322835346675-0.3491367787820.750287635141-0.1940978929661.786949768050.0512704624869-0.4485845490410.1029858565040.237017873060.0562818833640.09918564668430.03130716388630.140236571094-0.02161383649050.3228941902750.0463497440525-0.02154311912310.371169932091-0.04460448029190.256826672608-28.779489562-0.0079469194620858.1068446682
30.852812132829-0.301457761107-0.5667058321390.422064847883-0.235306292111.161690874880.01726714847770.204323341386-0.145563546921-0.146226583277-0.17850524989-0.02686812273570.173721756425-0.0217728475198-0.002428451841660.412133319858-0.0497301339576-0.08026596798090.253709641561-0.06541269251570.274400889015-19.4794348155-14.40999541362.53058851409
41.145971978270.228243931402-0.7268282984090.74682156492-0.415293821220.820010234-0.161417243-0.156273375392-0.08985182715720.1015374268960.04675437540060.1577071703770.1733505803580.0458900569541-0.04171667078310.2893994811890.004016386343280.03669003033810.320766583888-0.02823600517040.310007153472-42.7983525374-11.963689271248.3244790099
50.7246566947360.0174304393941-0.4381460185620.387757934211-0.2945282775691.269222818740.2121837925410.2461453322090.222008989274-0.04433025422-0.0557162321905-0.00226850395737-0.170302849616-0.000108944833193-0.09841772003550.355636998979-0.02177226595420.019368341620.225481113065-0.001676752308290.35229556153-16.80926802117.34991041775.44927656377
61.26427582938-0.441908868294-0.6392328928790.3470547267870.2735727951741.3970915916-0.0396032311899-0.0451239563027-0.01229081260310.0935713748454-0.01437377776110.151340588813-0.309486375832-0.336188887833-0.1420767414230.3616833528190.002244081223510.03011500132630.284118797612-0.03293269820310.396002494279-44.63364980798.8902518637247.665242135
72.113779462530.3847127098690.09147110995871.331262956790.1934530619531.411701341290.4065781178260.212578669419-0.4453335251710.0848640533051-0.1495743746970.1868453837060.421986947983-0.393632774407-0.0454605387760.413740407382-0.0933332273651-0.03246220851370.4827741514710.0470822047210.448474586607-65.3857556585-32.121626457839.4321592707
80.5819013162520.2229720495930.1681372893630.584852089067-0.6910333128681.81894941310.1021417286750.9372008247010.3128159404590.00638382745218-0.283268307404-0.229139490671-0.0910004459814-0.145339872802-0.06897627995260.4883471364340.1233238343970.02058699018650.8936071993890.1686243087340.427188432034-58.0339126578-18.248737356624.1329509992
90.249908621675-0.0283915000085-0.23867227792.1218473046-0.4352754715980.3258912387660.0826163953505-0.4321950027681.40645534619-0.1986466647730.0874183556204-0.0112008659737-0.3344770510220.1515729948430.3950189261680.578172403298-0.02280065727040.3098168624890.532224342263-0.2637119344921.58264175464-50.985072552339.575375635748.4029931775
101.024262273580.475945616584-0.4224535028260.565792237429-0.1617302042360.2901421711260.359711303664-0.05281781945370.8702832787-0.287054309930.056395875822-0.199377184928-0.5315381265820.727142850029-0.05940041595930.645960252639-0.1696416238550.213453301360.957097113085-0.2424492610891.47593679083-30.70352451633.320736764342.9261548591
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA8 - 4021
22chain BBB1 - 1721 - 172
33chain CCC8 - 5021
44chain DDD1 - 1721 - 172
55chain EEE8 - 5011
66chain FFF1 - 1721 - 172
77chain GGG31 - 1541 - 124
88chain HHH43 - 1491 - 107
99chain III31 - 1541 - 124
1010chain JJJ43 - 1491 - 107

+
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