Clue 1: Orient yourself
What are the main parts, stages, or choices in this model?
Use the labels and the picture's left-to-right, near-to-far, or before-and-after order. Name only what you can point to.
The question
How can a tool's shape show which job each part is built to do?
Why it matters: Protein-shape models help researchers choose which region to test, mutate, or target. Treating a prediction as proof can waste experiments or misstate what a variant does.
On your WebXam
You can connect a protein region's shape to its job without claiming more than the model shows.
For life
Turn the amount up and down; the result tells you if the signal decides or just allows.
Principle: Boss or doorman?
Try the everyday version first
Boss or doorman?
A multi-tool has separate parts shaped for cutting, gripping, and turning. Shape can suggest a part's job, but a picture cannot prove the tool completed a task.
Do not jump to the biology yet. Treat the picture as a small system. Track its parts, follow one change at a time, and keep more than one explanation open until the picture supplies a way to separate them.
Clue 2: Trace one change
What changes while the other parts stay the same?
Follow one object, stage, or path. Point to the first place where the situation changes instead of jumping to the ending.
Clue 3: Keep the cause open
What check would separate two explanations that still fit the picture?
List more than one explanation that still fits. Name the extra observation that would help you separate those possibilities.
Now inspect the illustration
Work from the visible evidence. A useful answer names the part of the picture that supports it and leaves unknown causes open.
- 1What are the main parts, stages, or choices in this model?
- 2What changes while the other parts stay the same?
- 3What check would separate two explanations that still fit the picture?
Tier 1 check
Finish with the everyday model
Use the multi-tool to connect one part's shape to a possible job without claiming more than the picture shows.
Answer in plain words. You can finish this required check without opening either optional section below.
Ready for the real names? Optional tier 2
Craniofacial Research Track
Session 12Reading the Evidence, DecemberLens: Human Body Systems
AlphaFold and UniProt: structure tells function
Discovery question
How can a tool's shape show which job each part is built to do?
Boss or doorman? A working shape may allow a job without deciding the whole outcome. Shape shows what is possible, not what happened in one child.
Before this page, you should know
- lines up two sequences position by position and reports , how much of the sequence matches.
- A is the same gene or in another species, descended from a shared ancestor.
If not, review
Today's new idea is only
Boss or doorman? A working shape may allow a job without deciding the whole outcome. Shape shows what is possible, not what happened in one child.
Goal: Inspect a three-dimensional model, identify one working region, and explain how its shape supports a specific job without overclaiming.
Know by the end
- predicts a 's 3D structure and colors each part by confidence (pLDDT), dark blue is very high, orange is low.
- A domain is a distinct functional part of a ; IRF6 has a near its front (N-terminal) end.
- UniProt lists a 's domains and features with exact amino acid positions.
- The is what lets IRF6 act as a , so its shape explains its job.
1
See the shape
Model start: shows IRF6 as a folded chain with a compact region near one end and a less structured tail.
- Open the entry for O14896 and describe the overall shape in one sentence.
- Read the Model Confidence key and write what dark blue means versus orange.
2
Find the working part
Model start: UniProt lists a near the front of the ; on that region is mostly dark blue, meaning high confidence.
- On UniProt, open the Family and Domains section and write the name and amino acid range of the .
- Back on , look at the coloring over that domain. Is the model confident there?
3
Structure to function
- Write one sentence linking the 's shape to IRF6's job as a .
- Predict: if a changed the shape of the , what could go wrong for the cell?
alphafold
- Open the entry at https://alphafold.ebi.ac.uk/entry/O14896 (O14896 is the UniProt accession for human IRF6).
- Look at the 3D viewer on the right. Use your mouse to rotate the structure (click and drag) and zoom (scroll) so you can see the whole fold.
- Find the Model Confidence key beside the viewer. Note the colors: dark blue is Very high (pLDDT over 90), light blue is Confident, yellow is Low, orange is Very low.
- Identify the compact, mostly dark-blue region near one end of the chain. This is the structured core that contains the .
- Open UniProt at https://www.uniprot.org/uniprotkb/O14896/entry in a second tab.
- In the left-side menu click Family & Domains (you can also click Features). Find the entry and write down its amino acid range.
- Go back to and check the coloring over that same range. Confirm whether the model is confident (blue) there, which it should be for a folded domain.
Turn in: An annotated note: a one-sentence description of IRF6's overall shape, the name and amino acid range of the (from UniProt), a note on its confidence color, and one sentence linking the domain's shape to IRF6's job as a .
AlphaFold
Open the tool Shows a predicted 3D shape of a , colored by how confident the prediction is.
When you use this: Use this when you have a variant and want to see WHERE in the folded it lands, so you can judge whether it sits in a part that matters.
What the screen looks like
Step by step
- 1Open .ebi.ac.uk and search the accession O14896 (human IRF6), or open the entry directly.
- 2Rotate the 3D model and find the near the front of the .
- 3Read the confidence color of that region from the legend (dark blue means trust the shape).
Capture these fields
- Confidence color (pLDDT band): Dark blue = very high, light blue = confident, yellow/orange = low
- Domain you are looking at: The DNA-binding domain near the front of the protein
- Amino-acid range: Roughly residues 13-113
How to read it: Dark-blue regions are predicted well and you can trust their shape; yellow/orange regions are flexible or uncertain, so do not over-read them. A change inside a well-folded, high-confidence domain is more likely to matter than one in a floppy, low-confidence loop.
Lost? How to read AlphaFold confidence UniProt
Open the tool The reference record for a : its length, its domains, and what each part does.
When you use this: Use this when you need to know which PART of the a variant hits, so you can predict whether it breaks a working region.
What the screen looks like
Step by step
- 1Open uniprot.org and search IRF6 human, then open entry O14896.
- 2Scroll to the Family and Domains section.
- 3Read the length and which domains exist (for example the ).
Capture these fields
- Accession (the protein's ID): O14896
- Length (amino acids): 467 aa
- Domains / regions: A DNA-binding domain and a protein-partner (SMIR) domain
How to read it: The domains tell you which part of the does which job. A variant that lands inside the is more likely to break IRF6's -factor function than one in a spacer region.
Lost? UniProt help: reading protein domains NCBI Gene
Open the tool The full reference record for a gene: its official symbol, ID, location, and what it does.
When you use this: Use this first, when you have a gene name and need its official ID and address. It is the home base every other database points back to.
What the screen looks like
Step by step
- 1Go to ncbi.nlm.nih.gov/gene and type the gene symbol IRF6 in the search box, then press Search.
- 2Open the top result whose organism is Homo sapiens (human).
- 3At the top of the record, read three things and write them down: the official symbol, the Gene ID number, and the location ( band).
Capture these fields
- Symbol (official gene name): IRF6
- Gene ID (the stable number): 3664
- Location (chromosome band): 1q32.2
- Summary (one line on its job): A transcription factor needed for the skin-surface cells that let the lip and palate fuse.
How to read it: The symbol and Gene ID let you find the exact same gene in every other database. The location should match the band you mapped (1q32). The summary tells you the gene's job in one sentence.
Lost? NCBI Gene help manual (how to use the Gene database)
Level 1, Guided
Use the sentence starters, a word bank from the vocabulary, a labeled diagram, and the exact source link.
Level 2, Collaborative
Complete a partly blank model or table and explain it.
Level 3, Independent
Make a claim from a new example or an unfamiliar entry in .
Team roles
- Manager: keeps the group moving
- Recorder: writes the shared model or table
- Evidence checker: verifies each claim against the source
- Reporter: explains the group's reasoning
Process reflection
- What evidence changed your thinking today?
- What did your group disagree about, and how did you resolve it?
- What question is still unresolved?
By the end of this session, submit ONE of: a labeled diagram with a 2-sentence explanation; a claim, evidence, reasoning paragraph; a completed data table from a real database; or a one-question exit ticket using today's vocabulary.
Recommended here: An annotated note: a one-sentence description of IRF6's overall shape, the name and amino acid range of the DNA-binding domain (from UniProt), a note on its AlphaFold confidence color, and one sentence linking the domain's shape to IRF6's job as a transcription factor.
Meets standard if your explanation correctly connects structure, timing, gene or protein function, or evidence source to Mateo's case: Inspect a three-dimensional model, identify one working region, and explain how its shape supports a specific job without overclaiming.
How this is graded (rubric)
For: An annotated note: a one-sentence description of IRF6's overall shape, the name and amino acid range of the DNA-binding domain (from UniProt), a note on its AlphaFold confidence color, and one sentence linking the domain's shape to IRF6's job as a transcription factor.
| Criterion | Proficient | Developing | Beginning |
|---|---|---|---|
| Complete | Every required part of the artifact is present and filled in. | Most parts are present, but one is missing or left blank. | Several parts are missing. |
| Accurate | The science and data are correct and match the evidence. | Mostly correct, with a small factual slip. | Key science or data is wrong. |
| Scientific reasoning (CER) | States a claim, backs it with specific evidence, and explains the reasoning. | Has a claim and evidence, but the reasoning is thin or missing. | Gives an answer with no evidence or reasoning. |
| Professional communication | Clear, organized, and labeled the way a clinician or scientist would write it. | Readable but disorganized or missing labels. | Hard to follow. |
| Submitted | Turned in through the route named under Submit here and confirmed. | Turned in, but in the wrong place or unconfirmed. | Not turned in. |
How the model answer scores against this rubric
- CompleteProficient: Nothing is left blank: the model fills every part of "An annotated note: a one-sentence description of IRF6's overall shape, the name and amino acid range of the DNA-binding domain (from UniProt), a note on its AlphaFold confidence color, and one sentence linking the domain's shape to IRF6's job as a transcription factor.".
- AccurateProficient: Every number and claim matches the case evidence.
- Scientific reasoning (CER)Proficient: It names a claim, cites the specific evidence, and explains the reasoning, not just the answer.
- Professional communicationProficient: It is organized and labeled like a real chart note.
- SubmittedProficient: It would be attached to your class form or handed in, and confirmed.
Go deeper Optional tier 3
Everything required is above. Open this section only if you want the research reading and source trail.
Student reading
The idea in plain English
How can a tool's shape show which job each part is built to do?
A multi-tool has separate parts shaped for cutting, gripping, and turning. Shape can suggest a part's job, but a picture cannot prove the tool completed a task.
Boss or doorman? A working shape may allow a job without deciding the whole outcome. Shape shows what is possible, not what happened in one child.
- predicts a 's 3D structure and colors each part by confidence (pLDDT), dark blue is very high, orange is low.
- A domain is a distinct functional part of a ; IRF6 has a near its front (N-terminal) end.
- UniProt lists a 's domains and features with exact amino acid positions.
- The is what lets IRF6 act as a , so its shape explains its job.
This lesson reading is written from the vetted sources in the advanced citation trail below.
Everything you need for today is on this page. These links are optional.
What to read
Read the short plain-language explanation written for this lesson. Plain-language reading for this session
Why this source matters
This explanation gives you the background for today's idea without making you decode a research paper: Boss or doorman? A working shape may allow a job without deciding the whole outcome. Shape shows what is possible, not what happened in one child.
Words to unlock first
Reading moves
- Skim the title and abstract first to get the gist.
- Circle the one sentence that states the main claim.
- Box the evidence the authors give for that claim.
- Mark one sentence that confuses you, and move on.
Stop point
Stop after the final 'Use it now' section. The research citations are available separately for advanced readers.
Your output
Write one claim-evidence sentence: state the main idea, then name the example or evidence that supports it.
These records and papers document the science. They are not assigned student reading. Use the plain-language lesson reading above unless your teacher asks you to inspect an original source.