[English] 日本語
Yorodumi
- EMDB-47215: Cryo-EM structure of Human Fibroblast Activation Protein alpha di... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47215
TitleCryo-EM structure of Human Fibroblast Activation Protein alpha dimer with one SUMO-I3 VHHs bound
Map dataFAP-1NB
Sample
  • Complex: Complex of Human Fibroblast activation protein alpha with SUMO-I3
    • Complex: Human Fibroblast activation protein alpha
      • Protein or peptide: Antiplasmin-cleaving enzyme FAP, soluble form
    • Complex: SUMO-I3
      • Protein or peptide: SUMO-I3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsFibroblast activation protein / single domain antibody / Protease / HYDROLASE
Function / homology
Function and homology information


negative regulation of extracellular matrix organization / melanocyte proliferation / peptidase complex / melanocyte apoptotic process / regulation of collagen catabolic process / negative regulation of cell proliferation involved in contact inhibition / prolyl oligopeptidase / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / basal part of cell ...negative regulation of extracellular matrix organization / melanocyte proliferation / peptidase complex / melanocyte apoptotic process / regulation of collagen catabolic process / negative regulation of cell proliferation involved in contact inhibition / prolyl oligopeptidase / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / basal part of cell / regulation of fibrinolysis / dipeptidyl-peptidase activity / lamellipodium membrane / positive regulation of execution phase of apoptosis / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / endothelial cell migration / serine-type peptidase activity / proteolysis involved in protein catabolic process / ruffle membrane / integrin binding / apical part of cell / lamellipodium / peptidase activity / protease binding / angiogenesis / endopeptidase activity / regulation of cell cycle / cell adhesion / serine-type endopeptidase activity / focal adhesion / cell surface / protein homodimerization activity / proteolysis / extracellular space / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Peptidase S9, serine active site / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Prolyl endopeptidase FAP
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsXu Z / Schnicker NJ / Wadas TJ
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R21-CA219899 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R21-CA227709 United States
Department of Defense (DOD, United States)W81XMH-19-1-0046 United States
CitationJournal: RSC Chem Biol / Year: 2025
Title: Cryo-electron microscopy reveals a single domain antibody with a unique binding epitope on fibroblast activation protein alpha.
Authors: Zhen Xu / Akesh Sinha / Darpan N Pandya / Nicholas J Schnicker / Thaddeus J Wadas /
Abstract: Fibroblast activation protein alpha (FAP) is a serine protease that is expressed at basal levels in benign tissues but is overexpressed in a variety of pathologies, including cancer. Despite this ...Fibroblast activation protein alpha (FAP) is a serine protease that is expressed at basal levels in benign tissues but is overexpressed in a variety of pathologies, including cancer. Despite this unique expression profile, designing functional diagnostic and therapeutic agents that effectively target this biomarker remains elusive. Here we report the structural characterization of the interaction between a novel single domain antibody (sdAb), I3, and FAP using cryo-electron microscopy. The reconstructions were determined to a resolution of 2.7 Å and contained two distinct populations; one I3 bound and two I3 molecules bound to the FAP dimer. In both cases, the sdAb bound a unique epitope that was distinct from the active site of the enzyme. Furthermore, this report describes the rational mutation of specific residues within the complementarity determining region 3 (CDR3) loop to enhance affinity and selectivity of the I3 molecule for FAP. This report represents the first sdAb-FAP structure to be described in the literature.
History
DepositionOct 8, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47215.png

Downloads & links

-
Map

FileDownload / File: emd_47215.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFAP-1NB
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å		0.86 Å/pix.
x 300 pix.
= 258. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.03392441 - 1.8202296
Average (Standard dev.)0.0017506471 (±0.029977595)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_47215_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_47215_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of Human Fibroblast activation protein alpha with SUMO-I3

EntireName: Complex of Human Fibroblast activation protein alpha with SUMO-I3
Components
  • Complex: Complex of Human Fibroblast activation protein alpha with SUMO-I3
    • Complex: Human Fibroblast activation protein alpha
      • Protein or peptide: Antiplasmin-cleaving enzyme FAP, soluble form
    • Complex: SUMO-I3
      • Protein or peptide: SUMO-I3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Complex of Human Fibroblast activation protein alpha with SUMO-I3

SupramoleculeName: Complex of Human Fibroblast activation protein alpha with SUMO-I3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 230 KDa

-
Supramolecule #2: Human Fibroblast activation protein alpha

SupramoleculeName: Human Fibroblast activation protein alpha / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: SUMO-I3

SupramoleculeName: SUMO-I3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Lama glama (llama)

-
Macromolecule #1: Antiplasmin-cleaving enzyme FAP, soluble form

MacromoleculeName: Antiplasmin-cleaving enzyme FAP, soluble form / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: dipeptidyl-peptidase IV
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.516211 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: RPSRVHNSEE NTMRALTLKD ILNGTFSYKT FFPNWISGQE YLHQSADNNI VLYNIETGQS YTILSNRTMK SVNASNYGLS PDRQFVYLE SDYSKLWRYS YTATYYIYDL SNGEFVRGNE LPRPIQYLCW SPVGSKLAYV YQNNIYLKQR PGDPPFQITF N GRENKIFN ...String:
RPSRVHNSEE NTMRALTLKD ILNGTFSYKT FFPNWISGQE YLHQSADNNI VLYNIETGQS YTILSNRTMK SVNASNYGLS PDRQFVYLE SDYSKLWRYS YTATYYIYDL SNGEFVRGNE LPRPIQYLCW SPVGSKLAYV YQNNIYLKQR PGDPPFQITF N GRENKIFN GIPDWVYEEE MLATKYALWW SPNGKFLAYA EFNDTDIPVI AYSYYGDEQY PRTINIPYPK AGAKNPVVRI FI IDTTYPA YVGPQEVPVP AMIASSDYYF SWLTWVTDER VCLQWLKRVQ NVSVLSICDF REDWQTWDCP KTQEHIEESR TGW AGGFFV STPVFSYDAI SYYKIFSDKD GYKHIHYIKD TVENAIQITS GKWEAINIFR VTQDSLFYSS NEFEEYPGRR NIYR ISIGS YPPSKKCVTC HLRKERCQYY TASFSDYAKY YALVCYGPGI PISTLHDGRT DQEIKILEEN KELENALKNI QLPKE EIKK LEVDEITLWY KMILPPQFDR SKKYPLLIQV YGGPCSQSVR SVFAVNWISY LASKEGMVIA LVDGRGTAFQ GDKLLY AVY RKLGVYEVED QITAVRKFIE MGFIDEKRIA IWGWSYGGYV SSLALASGTG LFKCGIAVAP VSSWEYYASV YTERFMG LP TKDDNLEHYK NSTVMARAEY FRNVDYLLIH GTADDNVHFQ NSAQIAKALV NAQVDFQAMW YSDQNHGLSG LSTNHLYT H MTHFLKQCFS LSDTGHHHHH HHHGGQ

UniProtKB: Prolyl endopeptidase FAP

-
Macromolecule #2: SUMO-I3

MacromoleculeName: SUMO-I3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 26.438318 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHGSL QDSEVNQEAK PEVKPEVKPE THINLKVSDG SSEIFFKIKK TTPLRRLMEA FAKRQGKEMD SLTFLYDGIE IQADQTPED LDMEDNDIIE AHREQIGGSD YKDDDDKLEV QLVESGGGLV QPGGSLRLSC AASGFTFSSY AMSWVRQAPG K GLEWVSAI ...String:
MHHHHHHGSL QDSEVNQEAK PEVKPEVKPE THINLKVSDG SSEIFFKIKK TTPLRRLMEA FAKRQGKEMD SLTFLYDGIE IQADQTPED LDMEDNDIIE AHREQIGGSD YKDDDDKLEV QLVESGGGLV QPGGSLRLSC AASGFTFSSY AMSWVRQAPG K GLEWVSAI NSGGGSTSYA DSVKGRFTIS RDNAKNTLYL QMNSLKPEDT AVYYCAKART GWSLAVPSFG SWGQGTQVTV SS

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.40 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris
150.0 mMsodium chlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.037 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 5450 / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing #1

Image processing ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 272711
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
Image processing #2

Image processing ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 272711
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

1z68

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
Output model

PDB-9dvq:
Cryo-EM structure of Human Fibroblast Activation Protein alpha dimer with one SUMO-I3 VHHs bound

+
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