[English] 日本語
Yorodumi
- EMDB-71135: Structure of MAb PhtD3 in complex with PhtD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-71135
TitleStructure of MAb PhtD3 in complex with PhtD
Map data
Sample
  • Complex: MAb PhtD3 fab complex with Pneumococcal histidine triad protein D.
    • Complex: MAb PhtD3 fab light chain.
      • Protein or peptide: MAb PhtD3 antibody light chain
    • Complex: MAb PhtD3 fab heavy chain.
      • Protein or peptide: MAb PhtD3 antibody heavy chain
    • Complex: Pneumococcal histidine triad protein D.
      • Protein or peptide: Histidine triad protein D
  • Ligand: ZINC ION
KeywordsA complex of an antibody / PhtD3 / with Pneumococcal histidine triad protein D / PhtD. / ANTIMICROBIAL PROTEIN
Function / homologyStreptococcal histidine triad repeat / Histidine triad protein / PhtA domain superfamily / Streptococcal histidine triad protein / Histidine triad protein D
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsDu J / Cui J / Lin Z / Eisenhauer J / Weiner DB / Pallesen J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI141236 United States
CitationJournal: To Be Published
Title: Fc-engineering and structural characterization of a broadly reactive monoclonal antibody targeting the pneumococcal histidine triad protein D (PhtD) on the surface of Streptococcus pneumoniae
Authors: Eisenhauer J / Gingerich AD / Du J / Parzych EM / Li Y / McCormick AL / Lin ZJ / Cui J / Cassel J / Bhardwaj B / Chu JD / Smith T / Patel A / Mousa JJ / Pallesen J / Weiner DB
History
DepositionJun 10, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_71135.png

Downloads & links

-
Map

FileDownload / File: emd_71135.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 280 pix.
= 266. Å		0.95 Å/pix.
x 280 pix.
= 266. Å		0.95 Å/pix.
x 280 pix.
= 266. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-0.16978452 - 17.884164999999999
Average (Standard dev.)-0.06850208 (±0.2953803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 266.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_71135_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_71135_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_71135_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MAb PhtD3 fab complex with Pneumococcal histidine triad protein D.

EntireName: MAb PhtD3 fab complex with Pneumococcal histidine triad protein D.
Components
  • Complex: MAb PhtD3 fab complex with Pneumococcal histidine triad protein D.
    • Complex: MAb PhtD3 fab light chain.
      • Protein or peptide: MAb PhtD3 antibody light chain
    • Complex: MAb PhtD3 fab heavy chain.
      • Protein or peptide: MAb PhtD3 antibody heavy chain
    • Complex: Pneumococcal histidine triad protein D.
      • Protein or peptide: Histidine triad protein D
  • Ligand: ZINC ION

-
Supramolecule #1: MAb PhtD3 fab complex with Pneumococcal histidine triad protein D.

SupramoleculeName: MAb PhtD3 fab complex with Pneumococcal histidine triad protein D.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Streptococcus pneumoniae (bacteria)

-
Supramolecule #2: MAb PhtD3 fab light chain.

SupramoleculeName: MAb PhtD3 fab light chain. / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Details: Fab fragment generated by proteolytic cleavage of mAb PhtD3 antibody.
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: MAb PhtD3 fab heavy chain.

SupramoleculeName: MAb PhtD3 fab heavy chain. / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Details: Fab fragment generated by proteolytic cleavage of mAb PhtD3 antibody.
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #4: Pneumococcal histidine triad protein D.

SupramoleculeName: Pneumococcal histidine triad protein D. / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Streptococcus pneumoniae (bacteria)

-
Macromolecule #1: Histidine triad protein D

MacromoleculeName: Histidine triad protein D / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pneumoniae (bacteria)
Molecular weightTheoretical: 93.795492 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKINKKYLAG SVAVLALSVC SYELGRHQAG QVKKESNRVS YIDGDQAGQK AENLTPDEVS KREGINAEQI VIKITDQGYV TSHGDHYHY YNGKVPYDAI ISEELLMKDP NYQLKDSDIV NEIKGGYVIK VDGKYYVYLK DAAHADNIRT KEEIKRQKQE R SHNHNSRA ...String:
MKINKKYLAG SVAVLALSVC SYELGRHQAG QVKKESNRVS YIDGDQAGQK AENLTPDEVS KREGINAEQI VIKITDQGYV TSHGDHYHY YNGKVPYDAI ISEELLMKDP NYQLKDSDIV NEIKGGYVIK VDGKYYVYLK DAAHADNIRT KEEIKRQKQE R SHNHNSRA DNAVAAARAQ GRYTTDDGYI FNASDIIEDT GDAYIVPHGD HYHYIPKNEL SASELAAAEA YWNGKQGSRP SS SSSYNAN PAQPRLSENH NLTVTPTYHQ NQGENISSLL RELYAKPLSE RHVESDGLIF DPAQITSRTA RGVAVPHGNH YHF IPYEQM SELEKRIARI IPLRYRSNHW VPDSRPEQPS PQSTPEPSPS LQPAPNPQPA PSNPIDEKLV KEAVRKVGDG YVFE KNGVS RYIPAKDLSA ETAAGIDSKL AKQESLSHKL GAKKTDLPSS DREFYNKTYD LLARIHQDLL DNKGRQVDFE ALDNL LERL KDVSSDKVKL VDDILAFLAP IRHPERLGKP NAQITYTDDE IQVAKLAGKY TTEDGYIFDP RDITSDEGDA YVTPHM THS HWIKKDSLSE AERAAAQAYA KEKGLTPPST DHQDSGNTEA KGAEAIYNRV KAAKKVPLDR MPYNLQYTVE VKNGSLI IP HYDHYHNIKF EWFDEGLYEA PKGYTLEDLL ATVKYYVEHP NERPHSDNGF GNASDHVRKN KADQDSKPDE DKGHDEVS E PTHPESDEKE NHAGLNPSAD NLYKPSTDTE ETEEEAEDTT DEAEIPQVEH SVINAKIADA EALLEKVTDP SIRQNAMET LTGLKSSLLL GTKDNNTISA EVDSLLALLK KSQPAPIQ

UniProtKB: Histidine triad protein D

-
Macromolecule #2: MAb PhtD3 antibody light chain

MacromoleculeName: MAb PhtD3 antibody light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.767754 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVLQTQVFIS LLLWISGAYG EIVLTQSPGT LSLSPGERAT LSCRASQSLT DNYLAWYQQK PGQAPRLLIY AASTRATGIP DRFSGSGSG TDFTLTISRL EPEDFAVYYC QQYQNSPFTF GGGKTVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ ...String:
MVLQTQVFIS LLLWISGAYG EIVLTQSPGT LSLSPGERAT LSCRASQSLT DNYLAWYQQK PGQAPRLLIY AASTRATGIP DRFSGSGSG TDFTLTISRL EPEDFAVYYC QQYQNSPFTF GGGKTVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

-
Macromolecule #3: MAb PhtD3 antibody heavy chain

MacromoleculeName: MAb PhtD3 antibody heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.877488 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDWTWRILFL VAAATGTHAQ VQLVQSGAEV KKPGSSVKVS CKASGAAFES FAFAWVRQAP GQGLEWMGRI IPILETRDYA QKFQGRVTI TADESTSTAY MELSSLRSED TAVYFCARDG HIMRTTLSDA ALDVWGQGTT VTVSSASTKG PSVFPLAPSS K STSGGTAA ...String:
MDWTWRILFL VAAATGTHAQ VQLVQSGAEV KKPGSSVKVS CKASGAAFES FAFAWVRQAP GQGLEWMGRI IPILETRDYA QKFQGRVTI TADESTSTAY MELSSLRSED TAVYFCARDG HIMRTTLSDA ALDVWGQGTT VTVSSASTKG PSVFPLAPSS K STSGGTAA LGCLVKDYFP EPVTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DK RVEPKSC DKTHTCPPCP APELLGGPSV FLFPPKPKDT LMISRTPEVT CVVVDVSHED PEVKFNWYVD GVEVHNAKTK PRE EQYNST YRVVSVLTVL HQDWLNGKEY KCKVSNKALP APIEKTISKA KGQPREPQVY TLPPSREEMT KNQVSLTCLV KGFY PSDIA VEWESNGQPE NNYKTTPPVL DSDGSFFLYS KLTVDKSRWQ QGNVFSCSVM HEALHNHYTQ KSLSLSPGK

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

+
Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3zfj

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1058309
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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