[English] 日本語
Yorodumi
- PDB-7trh: Human antibody K03.28 in complex with the influenza hemagglutinin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7trh
TitleHuman antibody K03.28 in complex with the influenza hemagglutinin head domain of A/California/07/2009(H1N1)(X-181)
Components
  • Hemagglutinin
  • K03.28 Fab heavy chain
  • K03.28 Fab lambda light chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / influenza / antibody / neutralizing / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN 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 / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMcCarthy, K.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Plos Biol. / Year: 2023
Title: A new class of antibodies that overcomes a steric barrier to cross-group neutralization of influenza viruses.
Authors: Simmons, H.C. / Watanabe, A. / Oguin Iii, T.H. / Van Itallie, E.S. / Wiehe, K.J. / Sempowski, G.D. / Kuraoka, M. / Kelsoe, G. / McCarthy, K.R.
History
DepositionJan 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: Hemagglutinin
H: K03.28 Fab heavy chain
B: K03.28 Fab lambda light chain


Theoretical massNumber of molelcules
Total (without water)73,9753
Polymers73,9753
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-27 kcal/mol
Surface area28410 Å2
Unit cell
Length a, b, c (Å)75.830, 43.650, 96.910
Angle α, β, γ (deg.)90.000, 105.033, 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

#1: Protein Hemagglutinin


Mass: 25198.215 Da / Num. of mol.: 1 / Fragment: head domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus
Strain: A/reassortant/NYMC X-181(California/07/2009 x NYMC X-157)(H1N1)
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C9EL84
#2: Antibody K03.28 Fab heavy chain


Mass: 25628.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody K03.28 Fab lambda light chain


Mass: 23148.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% (w/v) poly(ethylene glycol) 1500

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→46.8 Å / Num. obs: 24401 / % possible obs: 98.33 % / Redundancy: 2 % / Biso Wilson estimate: 77.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.03992 / Net I/σ(I): 14.93
Reflection shellResolution: 3→3.107 Å / Rmerge(I) obs: 0.3816 / Num. unique obs: 2401 / CC1/2: 0.771 / CC star: 0.933

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UBE, 6E56, 4HK0, 4WUK

3ube

6e56

4hk0

4wuk


Resolution: 3→46.8 Å / SU ML: 0.4575 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2424 623 5.01 %
Rwork0.2017 11816 -
obs0.2038 12439 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.52 Å2
Refinement stepCycle: LAST / Resolution: 3→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4971 0 0 0 4971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00285103
X-RAY DIFFRACTIONf_angle_d0.62576952
X-RAY DIFFRACTIONf_chiral_restr0.045762
X-RAY DIFFRACTIONf_plane_restr0.0064891
X-RAY DIFFRACTIONf_dihedral_angle_d4.9176698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.30.32851530.28892910X-RAY DIFFRACTION98.17
3.3-3.780.32061550.24792932X-RAY DIFFRACTION98.66
3.78-4.760.22961550.18322950X-RAY DIFFRACTION98.57
4.76-46.80.19361600.17323024X-RAY DIFFRACTION98.03
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)
13.39276649769-3.104709217091.230329310083.356626371820.07228017246883.22198946124-0.104286878208-0.2651421347041.27391759945-0.7126472822830.113401706165-1.0798199797-0.9511095951460.0883992475696-0.167814848410.9548956870940.179862600569-0.1129994256491.07643176441-0.4895246377320.80648039675230.915199192510.182074721816.9517491893
21.504514992151.1201645975-0.4525445438122.83626250925-0.5666831133932.812188810830.378731616683-0.45506535404-0.218369255731-0.230747107753-0.107337347776-0.318530119261-0.855584065675-0.8285121247730.6175551192490.8146727010930.103764582564-0.1369948553361.0501009584-0.4012798488160.62886936279932.083117385511.237189265816.7089756605
35.893381886682.910183106274.940664578924.064776025720.06789913278868.04518135272-0.395879461392-0.5438306046650.2692704445390.1230099449-1.009153584150.0263253420677-1.01062538111-0.751838868374-3.813359543640.6914114718670.0224808656462-0.05086314055961.594139754580.003091177482710.46626282673520.78090363930.17446007545316.0797825735
42.624635060060.08538227808551.274274689841.35207234279-0.6463468955880.953008628542-0.0950558617757-0.408319484398-0.262137693622-0.1164994094950.00663006195309-0.150900172695-0.300972511449-0.320068404893-0.0002511745628020.5692397641770.09451542257260.04896383118510.689616549638-0.02433443084930.62602033418131.482648916-3.458098061045.90384609029
51.257813241610.758014902655-0.1110605401251.129501766751.006640194771.701520356570.206827926248-0.862126167735-0.3424281714050.244584378809-0.140096808757-0.01796026207060.0768205827471-0.3279939429390.0001783781997530.6668299645270.007529139251710.02353456641760.8003969047550.1580887035140.76693682609126.4122731571-9.5985289572510.9313074881
63.337272458370.6786537074531.352625818960.9536537569160.8648216951322.29236946078-0.00574578311974-0.274065532651-0.642531521920.07540792075420.1070773399470.1397970470240.32450382775-0.2460839382960.0003277954541560.496873503081-0.01200208719220.06481628754860.3706745593870.08380435372390.570674082772-1.87047012351-7.31485211894-17.7821964877
70.9111707448230.1125913082130.04776729145180.2207381338930.1465865232140.723841075245-0.00926737141947-0.218464987943-0.280976164051-0.2774619665890.327993960022-0.03037127181270.174702957891-0.001854166315840.0001325931387830.598377101786-0.1090101925260.002823753276520.484128314688-0.02305434563650.498467488027-2.389675318841.82516637784-24.3164190196
80.7511152747710.6925232087410.1769015357851.34199106036-0.4794937455570.606252584843-0.321846325458-0.112556327318-0.44133988496-0.56715878690.347082262685-0.463122289470.5758928692010.7654199108990.005708310340010.792142516636-0.169565074660.1284502388890.8892747866-0.01298545068660.6154449605-7.9822895692212.0352640045-46.0891775379
90.3342762735050.2753605351360.1445933433980.4975055558510.4541735004910.501765767008-0.3704640006880.709913757181-0.155207050369-0.9635107627650.09779752423970.05934159065240.3302610868890.0426916302919-0.0003002454911191.18416553448-0.2822271160010.07556024938830.983780808227-0.08080263412130.725395848375-9.9010938990913.4455390477-54.457900152
102.340153176710.8118605198121.143962778461.58407363715-0.4234780679731.68256293535-0.265461423844-0.2112043399750.740555173706-0.03634530269930.239251990059-0.2706762691640.07926105714390.160937772491-0.003668239853610.5090043370310.0678934637859-0.02978224741350.473588392877-0.172224490890.66475787204314.81654868369.9269204704-16.4990702781
111.76123828086-0.6608660225521.157124022670.739723291039-0.9204973015931.2567621895-0.202158946519-0.01561284876790.6892489652430.3663561337780.1344777722940.0057915014551-0.3238312955790.08937466981380.01855829318940.5903090772810.01402843191620.0007376168062260.496794074631-0.0606400785990.64898126291311.291125356512.0809026937-20.5225144119
121.723045350591.12125688623-0.2858750682523.24022252619-0.105643255861.84238369906-0.107021420991-0.1247020813430.0932934500606-0.160944276759-0.03822110702130.0981214145299-0.0111005749504-0.04266638413940.0003689245490430.633413549975-0.152793804147-0.03289288184730.6055104623810.05986764457130.51717647632-8.6747439383726.3245183241-40.4584784668
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'G' and (resid 57 through 71 )GA57 - 711 - 15
22chain 'G' and (resid 72 through 91 )GA72 - 9116 - 35
33chain 'G' and (resid 92 through 104 )GA92 - 10436 - 48
44chain 'G' and (resid 105 through 174 )GA105 - 17449 - 122
55chain 'G' and (resid 175 through 264 )GA175 - 264123 - 212
66chain 'H' and (resid 2 through 83 )HB2 - 831 - 82
77chain 'H' and (resid 84 through 147 )HB84 - 14783 - 141
88chain 'H' and (resid 148 through 188 )HB148 - 188142 - 182
99chain 'H' and (resid 189 through 228 )HB189 - 228183 - 222
1010chain 'B' and (resid 1 through 68 )BC1 - 681 - 68
1111chain 'B' and (resid 69 through 117 )BC69 - 11769 - 117
1212chain 'B' and (resid 118 through 214 )BC118 - 214118 - 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