[English] 日本語
Yorodumi
- PDB-6q0l: Inferred intermediate I-7 (I-7-1) of the human antibody lineage 6... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q0l
TitleInferred intermediate I-7 (I-7-1) of the human antibody lineage 652 in complex with influenza hemagglutinin head domain of A/Beijing/262/95(H1N1)
Components
  • Fab heavy chain
  • Fab lambda chain
  • Hemagglutinin
KeywordsIMMUNE SYSTEM / 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 / 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 / membrane
Similarity search - Function
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 ...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
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMcCarthy, K.R. / Harrison, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089618 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI117892 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Affinity maturation in a human humoral response to influenza hemagglutinin.
Authors: McCarthy, K.R. / Raymond, D.D. / Do, K.T. / Schmidt, A.G. / Harrison, S.C.
History
DepositionAug 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin
H: Fab heavy chain
L: Fab lambda chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,08712
Polymers74,0003
Non-polymers1,0879
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: biolayer interferometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-29 kcal/mol
Surface area29540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.590, 70.280, 191.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Antibody , 2 types, 2 molecules HL

#2: Antibody Fab heavy chain


Mass: 25731.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody Fab lambda chain


Mass: 22930.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293F / Production host: Homo sapiens (human)

-
Protein / Sugars , 2 types, 3 molecules A

#1: Protein Hemagglutinin


Mass: 25338.191 Da / Num. of mol.: 1 / Fragment: Head domain, residues 65-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Beijing/262/1995(H1N1))
Strain: A/Beijing/262/1995(H1N1) / Gene: HA / Cell line (production host): BTI-Tn-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B4UPF7
#4: 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.: 2
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

-
Non-polymers , 2 types, 56 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM ammonium sulfate, 20% (w/v) PEG 4000, 100 mM CHES
PH range: 9

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→49.34 Å / Num. obs: 27683 / % possible obs: 99.88 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0753 / Net I/σ(I): 18.34
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 1.002 / Num. unique obs: 2708 / CC1/2: 0.814

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.34 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.52
RfactorNum. reflection% reflection
Rfree0.2597 1417 5.12 %
Rwork0.2169 --
obs0.2191 27668 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 176.91 Å2 / Biso mean: 70.1815 Å2 / Biso min: 28.54 Å2
Refinement stepCycle: final / Resolution: 2.5→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5032 0 70 49 5151
Biso mean--90.12 58.8 -
Num. residues----658
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5-2.58920.35161300.32372573
2.5892-2.69290.38311260.30632590
2.6929-2.81550.33891580.29792561
2.8155-2.96390.3331360.27352580
2.9639-3.14950.30821410.272605
3.1495-3.39270.33171330.25832632
3.3927-3.7340.28041410.22122605
3.734-4.2740.23831530.19132617
4.274-5.38380.18541520.16992680
5.3838-49.340.23831470.19352808
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)
13.9381.96284.89092.25223.02076.41210.006-1.28131.08470.1296-0.38430.5464-0.4813-1.62630.39110.6713-0.05960.15761.0501-0.24170.8235-9.329715.2009124.0599
27.1334-1.29986.43682.1335-2.38866.6141-0.276-1.14950.18151.5890.34361.0735-0.6513-1.5196-0.38170.926-0.19070.32871.15770.00740.7442-19.43235.4016118.9849
34.4048-0.39143.51943.90120.59263.02040.4565-0.41180.06720.2855-0.1548-0.01190.9645-0.8005-0.0860.638-0.03210.03850.70930.0590.554-3.75244.0705116.7227
44.46120.72442.65992.09671.23184.6110.7776-0.2584-0.36630.3267-0.3735-0.15491.2349-0.4233-0.40010.8112-0.1291-0.00930.62590.13420.5222-9.6488-2.3957111.5553
53.597-0.94170.58244.4186-0.16355.5048-0.6639-0.0542-0.1877-0.06040.27930.0030.16490.83150.34030.55250.0958-0.01740.63480.04580.5766-12.5003-7.887668.7094
61.6524-0.7605-2.01031.53671.95944.2469-0.0624-0.3691-0.24460.45090.16940.02810.65610.0137-0.08660.5677-0.0767-0.0750.58370.07910.5121-17.2706-4.89977.6157
73.0206-1.50621.88772.7241.65194.6230.1156-0.09660.9444-0.5163-0.49010.8072-0.86941.09180.06540.6029-0.1796-0.04180.472-0.02330.52756.115113.139845.0662
85.23432.65560.18624.58021.08052.9308-0.05740.09970.008-0.11740.0399-0.01660.05280.10580.01620.362-0.0013-0.0440.2268-0.03870.31451.8815.191952.8855
92.7472-1.41432.33015.1945-0.22255.4011-0.024-0.43990.22240.4213-0.0173-0.0395-0.5763-0.23910.06340.4086-0.1115-0.00220.6106-0.07050.4498-18.746816.235381.6221
102.07890.229-2.2080.5168-0.51844.34530.0195-0.14010.0284-0.0629-0.03030.16110.0083-0.2132-0.02980.3575-0.0223-0.0510.45520.00660.4857-12.501713.320764.9712
112.9821-0.8911-1.23027.36091.44885.49010.04250.19820.14590.14390.1190.54280.0241-0.2093-0.12310.5336-0.061-0.00720.33340.03780.5632-7.024517.875743.514
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 52 through 86 )A52 - 86
2X-RAY DIFFRACTION2chain 'A' and (resid 87 through 101 )A87 - 101
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 135 )A102 - 135
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 263 )A136 - 263
5X-RAY DIFFRACTION5chain 'H' and (resid 1 through 17 )H1 - 17
6X-RAY DIFFRACTION6chain 'H' and (resid 18 through 136 )H18 - 136
7X-RAY DIFFRACTION7chain 'H' and (resid 137 through 151 )H137 - 151
8X-RAY DIFFRACTION8chain 'H' and (resid 152 through 233 )H152 - 233
9X-RAY DIFFRACTION9chain 'L' and (resid 2 through 74 )L2 - 74
10X-RAY DIFFRACTION10chain 'L' and (resid 75 through 132 )L75 - 132
11X-RAY DIFFRACTION11chain 'L' and (resid 133 through 214 )L133 - 214

+
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