an#body((igg):( - rcsb · 2018-05-02 ·...

An#body (IgG): Analyze the 3D structure of immunoglobulin IgG by assembling this paper model

Developed as part of the RCSB Collabora@ve Curriculum Development Program 2014.

Paper model Based on X-‐ray structure (PDB ID: 1igt)

Contents of ac#vity packet: Paper model template: pages 2-‐14 Assembling instruc@ons: pages 15 -‐28

Light Chain A | Domain 1


2

la

lb

lc

ld

le

lh

lg

lf

lg lf

lb la

lc

ld le

1A

1D

1H

1I

1B

1F

1E

1C

NH3 +

AL1

Chain A

AL2

1G

lh li

lj

li

lk

lj

lk

ll

ll

lm

ln

lm

ln

2E

Light Chain A | Domain 2


3

2F

2G

2A

2B

2C

COO-‐

AL

Chain A

AL4

AL3

2D

ha

hb

hc

hd

he

hh hg

hf

hg hf

hb ha

hc

hd he

1D

Heavy Chain B | Domain 1


4

hh

hi

NH3 +

1A

1C

1B

1E 1F

1G

1H

1I

Chain B

BH1

BH2

hj

hk

hl

hm

hn

hr

hq

ho

hp ho

hk hj

hl

hm

hn



5

hq

hp

hi

2A

2B

2C

2D

2F

2G

2E

Chain B

BH3

BH4

BH

BHA BHB

hs

ht

hu

hv

hw

hz

hy

hx

hy hx

ht hs

hu

hv hw



6

hz

haa

hr

3B

3C

3F

3E

3G

3D

3A

Chain B

BH5

BH6

BHC

hab

hac

had

hae

haf

hag

hag hac

hab

had

hae haf

Heavy Chain B |Domain 4


7

haa

COO-‐

4A

4B

4D

4C

4F

4G

4E

Chain B

BH7

BH8

la

lb

lc

ld

le

lh

lg

lf

lg lf

lb la

lc

ld le

1A

1D

1H

1I

Light Chain C | Domain 1


8

1B

1F

1E

1C

NH3 +

CL1

Chain C

CL2

1G

lh li

lj

li

lk

lj

lk

ll

ll

lm

ln

lm

ln

2E

Light Chain C | Domain 2


9

2F

2G

2A

2B

2C

COO-‐

CL

Chain C

CL4

CL3

2D

ha

hb

hc

hd

he

hh hg

hf

hg hf

hb ha

hc

hd he

Heavy Chain D | Domain 1


10

hh

hi

NH3 +

1A

1B

1E 1F

1G

1H

1I

Chain D

DH1

DH2

1C 1D

hj

hk

hl

hm

hn

hr

hq

ho

hp ho

hk hj

hl

hm

hn



11

hq

hp

hi

2A

2B

2C

2D

2F

2G

2E

Chain D

DH3

DH4

DH

DHA DHB

hs

ht

hu

hv

hw

hz

hy

hx

hy hx

ht hs

hu

hv hw



12

hz

haa

hr

3B

3C

3F

3E

3G

3D

3A

Chain D

DH5

DH6

DHC

hab

hac

had

hae

haf

hag

hag hac

hab

had

hae haf



13

haa

COO-‐

4A

4B

4D

4C

4F

4G

4E

Chain D

DH7

DH8

Disulfide Linkages


14

AL1 AL3

AL BH5

BH7 BH1

BH3

AL2

AL4

BH

BH2

BH4

BH6

BH8

BHB DHB

BHC DHC

BHA DHA CL1

CL3 CL

DH5 DH7

DH1 DH3

CL2

CL4

DH

DH2

DH4

DH6

DH8

An#body Model: Overview


15

The An@body consists of 4 chains:

•  2 light chains: A, C Each light chain is made up of 2 immunoglobulin domains

•  2 heavy chains: B, D Each heavy chain is made up of 4 immunoglobulin domains

Heavy Chain B

Light Chain A

Heavy Chain D

Light Chain C

An#body Model: Overview


16

Assembly Overview:

•  Each page from 2 to 13 contains elements to build 1 domain

•  You will fist create the domains and then assemble the chains

•  The an@body structure is stabilized by 17 disulfide linkages colored yellow on the image to the right

•  The stripes in the paper model template, on page 14, represent these linkages

•  Crea@ng the disulfide linkages is the last step in making each Ig domain and finally the complete an@body molecule.

Prepara#on

For each page from 2 to 13 : •  Cut out each strip along the

do\ed lines •  Note that the shaded regions

labeled ho, hk, etc. should be included in the strip

•  When crea@ng the domains, work on one page at a @me to avoid mixing up the strips.


17

Make sure these shaded regions remain a\ached to the strips

Immunoglobulin Domains

For each page from 2 to 13 : Step 1 Create the representa@on of the polymer backbone •  Tape together the strips into a long strand

•  The labels la, lb, etc. on the grey background should be hidden underneath the labels on the colored background


18

Find matching labels and tape together hiding the hatched grey label.

Polymer backbones for all 12 domains.


Step 2 Create Immunoglobulin Domains The solid black arrows labeled 1A, 1B, 1C, 1D etc. represent the beta strands. Create the beta strand clusters by taping together the strands side by side. For each domain, make sure that: 1.  The le[ers on the rectangular labels

are in alphabe#cal order, for example 4A-‐4B-‐4C-‐4D, or 4E-‐4F-‐4G. Note: Don’t connect the strips if there isn’t any grey area in between them.

2.  The grey area between the strands is aligned. (See next page)

3.  The beta strand arrows point up and down alternately (See next page)


19

The le\ers inside the rectangular labels follow alphabe@cal order

Note: No grey area. Stop here and begin a new cluster star@ng with 4E through 4G.



20

The gray area between strands is aligned.

The beta strand arrows point up and down alternately

All 12 domains assembled

Heavy and Light Chains

Assembling the 4 polymer chains:

Light Chains A and C: •  Tape together the 2 domains

of each chain at the label lh;

Heavy Chains B and C: •  Tape together the

4 domains of each chain at the labels hi, hr and haa


21

Note: Follow the chain labels to make

sure you are connec@ng the domains from the proper chains.

Align and tape; Grey labels should be hidden underneath the colored ones.

Light and Heavy Chains


22

2 light and 2 heavy polymer chains assembled

Disulfide Linkages

The Structure of An@body is stabilized by 2 types of disulfide linkages: •  12 Intradomain linkages

stabilize each of the 12 immunglobulin domains.

•  5 Interchain linkages hold the different chains together

•  The 17 strips on page 14 represent the disulfide linkages •  Cut out all strips on the

do\ed lines •  Fold down each strip on both

hatched regions.


23

Interchain Linkages

Intradomain Linkages (1 for each domain)

Disulfide Linkages

Create the Intradomain Disulfide Linkages: For each domain: •  Find corresponding labels on

the domains (round, marked AL1 and AL2) and on the linkages

•  Align the strip label underneath the domain’s round label and tape


24

Corresponding labels

The linkage strip labels are aligned

and taped underneath the

round labels

Disulfide Linkages

Note: Before you start the final step, it might be a good idea to align the light and heavy chains. Use the images on pages 15 (overview sec@on) for help with domain and chain placement in the model. This step will help with label iden@fica@on and proper placement of the interchain linkages.


25

Disulfide Linkages

Create the interchain disulfide linkages: •  Chains A and B: Iden@fy the round, do[ed labels AL and BH on the model and connect them with corresponding disulfide strip. The printed sides of the labels should face each other.

•  Repeat for chains C and D (labels CL and DH)


26

Chains are connected at round do\ed AL and BH labels.

The printed sides of the labels face each other.

Disulfide Linkages

Create the interchain disulfide linkages: Chains B and D: •  Iden@fy the do\ed round labels BHA–DHA BHB–DHB BHC–DHC on the model and on the disulfide strips

•  Tape the printed side of the hatched regions on top of the do\ed round labels.


27

Chains B and D are connected at round do\ed labels. The printed sides of the labels face each other.

Finished Model


28

Sugges#on: This model can be made as a group project. Assign each domain to a different individual. The 12 different domains in the an@body can be assembled together and all the disulfide bridges put in place as a group.

an#body((igg):( - rcsb · 2018-05-02 ·...

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