[English] 日本語
Yorodumi
- PDB-8txp: Crystal structure of 05.GC.w13.01 Fab in complex with H1 HA from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8txp
TitleCrystal structure of 05.GC.w13.01 Fab in complex with H1 HA from A/California/04/2009(H1N1)
Components
  • (GC_w13_A, Fab ...) x 2
  • (Hemagglutinin) x 2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / H1N1 / Antibody / Hemagglutinin / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / metal ion binding / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLin, T.H. / Moore, N. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: J Exp Med / Year: 2024
Title: Maturation of germinal center B cells after influenza virus vaccination in humans.
Authors: Katherine M McIntire / Hailong Meng / Ting-Hui Lin / Wooseob Kim / Nina E Moore / Julianna Han / Meagan McMahon / Meng Wang / Sameer Kumar Malladi / Bassem M Mohammed / Julian Q Zhou / Aaron ...Authors: Katherine M McIntire / Hailong Meng / Ting-Hui Lin / Wooseob Kim / Nina E Moore / Julianna Han / Meagan McMahon / Meng Wang / Sameer Kumar Malladi / Bassem M Mohammed / Julian Q Zhou / Aaron J Schmitz / Kenneth B Hoehn / Juan Manuel Carreño / Temima Yellin / Teresa Suessen / William D Middleton / Sharlene A Teefey / Rachel M Presti / Florian Krammer / Jackson S Turner / Andrew B Ward / Ian A Wilson / Steven H Kleinstein / Ali H Ellebedy /
Abstract: Germinal centers (GC) are microanatomical lymphoid structures where affinity-matured memory B cells and long-lived bone marrow plasma cells are primarily generated. It is unclear how the maturation ...Germinal centers (GC) are microanatomical lymphoid structures where affinity-matured memory B cells and long-lived bone marrow plasma cells are primarily generated. It is unclear how the maturation of B cells within the GC impacts the breadth and durability of B cell responses to influenza vaccination in humans. We used fine needle aspiration of draining lymph nodes to longitudinally track antigen-specific GC B cell responses to seasonal influenza vaccination. Antigen-specific GC B cells persisted for at least 13 wk after vaccination in two out of seven individuals. Monoclonal antibodies (mAbs) derived from persisting GC B cell clones exhibit enhanced binding affinity and breadth to influenza hemagglutinin (HA) antigens compared with related GC clonotypes isolated earlier in the response. Structural studies of early and late GC-derived mAbs from one clonal lineage in complex with H1 and H5 HAs revealed an altered binding footprint. Our study shows that inducing sustained GC reactions after influenza vaccination in humans supports the maturation of responding B cells.
History
DepositionAug 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 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
H: GC_w13_A, Fab heavy chain
L: GC_w13_A, Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5049
Polymers103,8954
Non-polymers2,6085
Water00
1
A: Hemagglutinin
B: Hemagglutinin
H: GC_w13_A, Fab heavy chain
L: GC_w13_A, Fab light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: GC_w13_A, Fab heavy chain
L: GC_w13_A, Fab light chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: GC_w13_A, Fab heavy chain
L: GC_w13_A, Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,51127
Polymers311,68612
Non-polymers7,82515
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area55160 Å2
ΔGint-138 kcal/mol
Surface area120360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.350, 128.350, 155.756
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin


Mass: 36729.402 Da / Num. of mol.: 1 / Fragment: HA1 subdomain (UNP residues 18-344)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: C3W5S1
#2: Protein Hemagglutinin


Mass: 20206.320 Da / Num. of mol.: 1 / Fragment: HA2 subdomain (UNP residues 326-499)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: I1ZFF9

-
Antibody , 2 types, 2 molecules HL

#3: Antibody GC_w13_A, Fab heavy chain


Mass: 23561.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody GC_w13_A, Fab light chain


Mass: 23397.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

-
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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium acetate, pH 6.2, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.75→45.24 Å / Num. obs: 38915 / % possible obs: 100 % / Redundancy: 16.2 % / CC1/2: 0.99 / Rpim(I) all: 0.035 / Rsym value: 0.137 / Net I/σ(I): 21.6
Reflection shellResolution: 2.76→2.8 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1962 / CC1/2: 0.56 / Rpim(I) all: 0.423 / Rsym value: 1 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4M4Y

4m4y


Resolution: 2.75→45.24 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2918 1962 5.05 %
Rwork0.2496 --
obs0.2517 38860 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7231 0 173 0 7404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037567
X-RAY DIFFRACTIONf_angle_d0.62110271
X-RAY DIFFRACTIONf_dihedral_angle_d7.991092
X-RAY DIFFRACTIONf_chiral_restr0.0441181
X-RAY DIFFRACTIONf_plane_restr0.0051301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.820.44491010.39552623X-RAY DIFFRACTION100
2.82-2.90.39811610.34712584X-RAY DIFFRACTION100
2.9-2.990.38371330.31972625X-RAY DIFFRACTION100
2.99-3.080.32931370.28772599X-RAY DIFFRACTION100
3.08-3.190.3391630.28842596X-RAY DIFFRACTION100
3.19-3.320.35181570.29852597X-RAY DIFFRACTION100
3.32-3.470.40741110.31492639X-RAY DIFFRACTION100
3.47-3.650.33341490.27252571X-RAY DIFFRACTION99
3.65-3.880.40111340.28092631X-RAY DIFFRACTION99
3.88-4.180.32061230.22922631X-RAY DIFFRACTION100
4.18-4.60.22941330.20992678X-RAY DIFFRACTION100
4.6-5.270.22361570.2012630X-RAY DIFFRACTION100
5.27-6.630.23561530.23692686X-RAY DIFFRACTION100
6.63-45.240.26271500.22942808X-RAY DIFFRACTION100

+
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